May. 10, 08:38:38 2013 Greetings, [ Text modified to reflect that this was run under PSVS - Aneerban Bhattacharya: Dec 2005 ] The following checks were made on : ----------------------------------------- DISTANCES AND ANGLES We have checked your intra and intermolecular distances and angles with the procedures currently in place at PDB: ==> The following solvent molecules are further away than 3.5 Angstroms from macromolecule atoms which are available for hydrogen bonding in the asymmetric unit. none The coordinates for water molecules which could be translated back into the asymmetric unit are listed. If you do not indicate otherwise we will replace the solvent coordinates in the entry with the ones below: none ==> Close contacts in same asymmetric unit. Distances smaller than 2.2 Angstroms are considered as close contacts. none ==> Close contacts based on crystal symmetry. Distances smaller than 2.2 Angstroms are considered as close contacts. none ==> Bond and angle checks are performed by first computing the average rms error for all bonds and angles relative to standard values for nucleotide units [L. Clowney et al., Geometric Parameters in Nucleic Acids: Nitrogenous Bases, J.Am.Chem.Soc. 1996, 118, 509-518; A. Gelbin et al., Geometric Parameters in Nucleic Acids: Sugar and Phosphate Constituents, J.Am.Chem.Soc. 1996, 118, 519-529] and amino acid units [R.A. Engh and R. Huber, Accurate Bond and Angle Parameters for X-ray protein structure refinement, Acta Crystallogr. 1991, A47, 392-400]. Any bond or angle which deviates from the dictionary values by more than six times this computed rms error is identified as an outlier. *** Covalent Bond Lengths: The RMS deviation for covalent bonds relative to the standard dictionary is 0.009 Angstroms The following table contains a list of the covalent bonds greater than 6.0*RMSD. Deviation Residue Chain Sequence AT1 - AT2 Bond Dictionary Name ID Number Distance Value ------------------------------------------------------------------------ -0.062 ARG A 23 CB - CG 1.458 1.520 *** Covalent Angle Values: The RMS deviation for covalent angles relative to the standard dictionary is 1.2 degrees. All covalent bond angles lie within a 6.0*RMSD range about the standard dictionary values. TORSION ANGLES The torsion angle distributions have been checked. The postscript file of the conformation rings showing the torsion angle distributions will be sent in a separate E-mail message. CHIRALITY The chirality has been checked and there are no incorrect carbon chiral centers. Some of O1P and O2P atoms do not follow the convention defined in the standard IUBMB nomenclature (Liebecq, C. Compendium of Biochemical Nomenclature and Related Documents, 2nd ed.; Portland Press: London and Chapel Hill, 1992). If you do not indicate otherwise, we will switch the labels of O1P and O2P as shown below. OTHER IMPORTANT ISSUES ==> Please check carefully REMARKS 3 and 200 and fill in the parameters as appropriate. ==> The following residues are missing: (Note: The SEQ number starts from 1 for each chain according to SEQRES sequence record.) RES MOD#C SEQ MSE( A -76 ) GLY( A -75 ) HIS( A -74 ) HIS( A -73 ) HIS( A -72 ) HIS( A -71 ) HIS( A -70 ) HIS( A -69 ) SER( A -68 ) HIS( A -67 ) MSE( A -66 ) LEU( A -65 ) PRO( A -64 ) PRO( A -63 ) GLU( A -62 ) GLN( A -61 ) TRP( A -60 ) SER( A -59 ) HIS( A -58 ) THR( A -57 ) THR( A -56 ) VAL( A -55 ) ARG( A -54 ) ASN( A -53 ) ALA( A -52 ) LEU( A -51 ) LYS( A -50 ) ASP( A -49 ) LEU( A -48 ) LEU( A -47 ) LYS( A -46 ) ASP( A -45 ) MSE( A -44 ) ASN( A -43 ) GLN( A -42 ) SER( A -41 ) SER( A -40 ) LEU( A -39 ) ALA( A -38 ) LYS( A -37 ) GLU( A -36 ) CYS( A -35 ) PRO( A -34 ) LEU( A -33 ) SER( A -32 ) GLN( A -31 ) SER( A -30 ) MSE( A -29 ) ILE( A -28 ) SER( A -27 ) SER( A -26 ) ILE( A -25 ) VAL( A -24 ) ASN( A -23 ) SER( A -22 ) THR( A -21 ) TYR( A -20 ) TYR( A -19 ) ALA( A -18 ) ASN( A -17 ) VAL( A -16 ) SER( A -15 ) ALA( A -14 ) ALA( A -13 ) LYS( A -12 ) CYS( A -11 ) GLN( A -10 ) GLU( A -9 ) PHE( A -8 ) GLY( A -7 ) ARG( A -6 ) TRP( A -5 ) TYR( A -4 ) LYS( A -3 ) HIS( A -2 ) PHE( A -1 ) LYS( A 0 ) LYS( A 1 ) THR( A 2 ) LYS( A 3 ) ASP( A 4 ) MSE( A 5 ) MSE( A 6 ) PDB Chain_ID: A 1 15 SEQRES: MSE GLY HIS HIS HIS HIS HIS HIS SER HIS MSE LEU PRO PRO GLU COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 16 30 SEQRES: GLN TRP SER HIS THR THR VAL ARG ASN ALA LEU LYS ASP LEU LEU COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 31 45 SEQRES: LYS ASP MSE ASN GLN SER SER LEU ALA LYS GLU CYS PRO LEU SER COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 46 60 SEQRES: GLN SER MSE ILE SER SER ILE VAL ASN SER THR TYR TYR ALA ASN COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 61 75 SEQRES: VAL SER ALA ALA LYS CYS GLN GLU PHE GLY ARG TRP TYR LYS HIS COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 76 90 SEQRES: PHE LYS LYS THR LYS ASP MSE MSE HIS HIS SER HIS MET LEU PRO COORDS: ... ... ... ... ... ... ... ... HIS HIS SER HIS MET LEU PRO 7 13 91 105 SEQRES: PRO GLU GLN TRP SER HIS THR THR VAL ARG ASN ALA LEU LYS ASP COORDS: PRO GLU GLN TRP SER HIS THR THR VAL ARG ASN ALA LEU LYS ASP 14 28 106 120 SEQRES: LEU LEU LYS ASP MET ASN GLN SER SER LEU ALA LYS GLU CYS PRO COORDS: LEU LEU LYS ASP MET ASN GLN SER SER LEU ALA LYS GLU CYS PRO 29 43 121 135 SEQRES: LEU SER GLN SER MET ILE SER SER ILE VAL ASN SER THR TYR TYR COORDS: LEU SER GLN SER MET ILE SER SER ILE VAL ASN SER THR TYR TYR 44 58 136 150 SEQRES: ALA ASN VAL SER ALA ALA LYS CYS GLN GLU PHE GLY ARG TRP TYR COORDS: ALA ASN VAL SER ALA ALA LYS CYS GLN GLU PHE GLY ARG TRP TYR 59 73 151 156 SEQRES: LYS HIS PHE LYS LYS THR COORDS: LYS HIS PHE LYS LYS THR 74 79 ==> The following residues have missing atoms: RES MOD#C SEQ ATOMS MET( A 11) SD MET( A 33) SD MET( A 48) SD ==> The following residues have extra atoms: RES MOD#C SEQ ATOMS MET( A 11) SE MET( A 33) SE MET( A 48) SE HR4435B_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 11) in Token 'HELIX' can not be found in coordinates HR4435B_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 11) in Token 'MODRES' can not be found in coordinates HR4435B_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 33) in Token 'MODRES' can not be found in coordinates HR4435B_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 48) in Token 'MODRES' can not be found in coordinates