May. 10, 04:38:08 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 0.005 Angstroms All covalent bonds lie within a 6.0*RMSD range about the standard dictionary values. *** Covalent Angle Values: The RMS deviation for covalent angles relative to the standard dictionary is 1.1 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 -77 ) ASN( A -76 ) LEU( A -75 ) THR( A -74 ) VAL( A -73 ) ASN( A -72 ) GLY( A -71 ) LYS( A -70 ) PRO( A -69 ) SER( A -68 ) THR( A -67 ) VAL( A -66 ) ASP( A -65 ) GLY( A -64 ) ALA( A -63 ) GLU( A -62 ) SER( A -61 ) LEU( A -60 ) ASN( A -59 ) VAL( A -58 ) THR( A -57 ) GLU( A -56 ) LEU( A -55 ) LEU( A -54 ) SER( A -53 ) ALA( A -52 ) LEU( A -51 ) LYS( A -50 ) VAL( A -49 ) ALA( A -48 ) GLN( A -47 ) ALA( A -46 ) GLU( A -45 ) TYR( A -44 ) VAL( A -43 ) THR( A -42 ) VAL( A -41 ) GLU( A -40 ) LEU( A -39 ) ASN( A -38 ) GLY( A -37 ) GLU( A -36 ) VAL( A -35 ) LEU( A -34 ) GLU( A -33 ) ARG( A -32 ) GLU( A -31 ) ALA( A -30 ) PHE( A -29 ) ASP( A -28 ) ALA( A -27 ) THR( A -26 ) THR( A -25 ) VAL( A -24 ) LYS( A -23 ) ASP( A -22 ) GLY( A -21 ) ASP( A -20 ) ALA( A -19 ) VAL( A -18 ) GLU( A -17 ) PHE( A -16 ) LEU( A -15 ) TYR( A -14 ) PHE( A -13 ) MSE( A -12 ) GLY( A -11 ) GLY( A -10 ) GLY( A -9 ) LYS( A -8 ) LEU( A -7 ) GLU( A -6 ) HIS( A -5 ) HIS( A -4 ) HIS( A -3 ) HIS( A -2 ) HIS( A -1 ) HIS( A 0 ) PDB Chain_ID: A 1 15 SEQRES: MSE ASN LEU THR VAL ASN GLY LYS PRO SER THR VAL ASP GLY ALA COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 16 30 SEQRES: GLU SER LEU ASN VAL THR GLU LEU LEU SER ALA LEU LYS VAL ALA COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 31 45 SEQRES: GLN ALA GLU TYR VAL THR VAL GLU LEU ASN GLY GLU VAL LEU GLU COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 46 60 SEQRES: ARG GLU ALA PHE ASP ALA THR THR VAL LYS ASP GLY ASP ALA VAL COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 61 75 SEQRES: GLU PHE LEU TYR PHE MSE GLY GLY GLY LYS LEU GLU HIS HIS HIS COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 76 90 SEQRES: HIS HIS HIS MET ASN LEU THR VAL ASN GLY LYS PRO SER THR VAL COORDS: ... ... ... MET ASN LEU THR VAL ASN GLY LYS PRO SER THR VAL 1 12 91 105 SEQRES: ASP GLY ALA GLU SER LEU ASN VAL THR GLU LEU LEU SER ALA LEU COORDS: ASP GLY ALA GLU SER LEU ASN VAL THR GLU LEU LEU SER ALA LEU 13 27 106 120 SEQRES: LYS VAL ALA GLN ALA GLU TYR VAL THR VAL GLU LEU ASN GLY GLU COORDS: LYS VAL ALA GLN ALA GLU TYR VAL THR VAL GLU LEU ASN GLY GLU 28 42 121 135 SEQRES: VAL LEU GLU ARG GLU ALA PHE ASP ALA THR THR VAL LYS ASP GLY COORDS: VAL LEU GLU ARG GLU ALA PHE ASP ALA THR THR VAL LYS ASP GLY 43 57 136 147 SEQRES: ASP ALA VAL GLU PHE LEU TYR PHE MET GLY GLY GLY COORDS: ASP ALA VAL GLU PHE LEU TYR PHE MET GLY GLY GLY 58 69 ==> The following residues have missing atoms: RES MOD#C SEQ ATOMS MET( A 1) SD MET( A 66) SD ==> The following residues have extra atoms: RES MOD#C SEQ ATOMS MET( A 1) SE MET( A 66) SE GMR137_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 1) in Token 'MODRES' can not be found in coordinates GMR137_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 66) in Token 'MODRES' can not be found in coordinates