                                                       May. 10, 11:51:17 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

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    1.2 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 have missing atoms:                        

     RES MOD#C SEQ          ATOMS

     GLU(    B  41)          CG   CD  OE1  OE2 
     GLU(    B  55)          CG   CD  OE1  OE2 
     SER(    B 124)          OG 
     LYS(    C  72)          CG   CD   CE   NZ 





LKR112_XRay_em_bcr3.pdb: Error: Z value is 12. It should be 8.


