Content:

• See also
• Deposited
• (Re-)refinement

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See also:

• RCSB
• PDBe
• PDBj

• PDB-REDO

• PDBpeep

    Diffraction limits & principal axes of ellipsoid fitted to diffraction cut-off surface:
    2.176         1.0000   0.0000   0.0000       a*
    1.907         0.0000   1.0000   0.0000       b*
    1.974         0.0000   0.0000   1.0000       c*

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Deposited

Date deposited	Date data collection	Resolution	R, Rfree
20170525	20151203	2.00	0.1910 0.2220

Molprobity (CCP4 7.0 version) summary:

Ramachandran outliers =   0.00 %   
              favored =  97.35 %   
Rotamer outliers      =   0.34 %   
C-beta deviations     =     1   
Clashscore            =   4.32   
RMS(bonds)            =   0.0050   
RMS(angles)           =   1.05   
MolProbity score      =   1.34   
Resolution            =   2.00   
R-work                =   0.1910   
R-free                =   0.2220   

Additional analysis:

Number of waters      =   411

<B> (all atoms) =   27.77 ( sd =   10.29 ) for       3271 non-hydrogen atoms
<B>   (protein) =   25.65 ( sd =    8.54 ) for       2703 non-hydrogen atoms
<B>     (water) =   35.48 ( sd =   10.68 ) for        411 non-hydrogen atoms
<B>    (others) =   44.00 ( sd =   12.41 ) for        157 non-hydrogen atoms

B min/max       (all non-hydrogen atoms) =    5.55 /   75.33
B min/max   (protein non-hydrogen atoms) =   10.73 /   69.85
B min/max     (water non-hydrogen atoms) =    5.55 /   63.02
B min/max     (other non-hydrogen atoms) =   18.83 /   75.33

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BUSTER (re-)refinement

Molprobity (CCP4 7.0 version) summary:

Ramachandran outliers =   0.00 %   
              favored =  96.47 %   
Rotamer outliers      =   1.03 %   
C-beta deviations     =     2   
Clashscore            =   1.80   
RMS(bonds)            =   0.0120   
RMS(angles)           =   1.63   
MolProbity score      =   1.18   
Resolution            =   2.00   
R-work                =   0.1833   
R-free                =   0.2236   

Additional analysis:

Number of waters      =   448

<B> (all atoms) =   27.10 ( sd =   10.59 ) for       3308 non-hydrogen atoms
<B>   (protein) =   24.18 ( sd =    7.48 ) for       2703 non-hydrogen atoms
<B>     (water) =   38.23 ( sd =   12.41 ) for        448 non-hydrogen atoms
<B>    (others) =   45.67 ( sd =   10.70 ) for        157 non-hydrogen atoms

B min/max       (all non-hydrogen atoms) =    6.80 /   78.18
B min/max   (protein non-hydrogen atoms) =    6.80 /   56.96
B min/max     (water non-hydrogen atoms) =    7.89 /   78.18
B min/max     (other non-hydrogen atoms) =   23.85 /   62.65

Refinement progression:

Results:

File	Remark
5VYH_aB_refine.01_03_refine.pdb.gz	exact refinement commands are in header
5VYH_aB_refine.01_03_refine.mtz.gz	including original deposited data and several re-refinement map coefficients
5VYH_aB_refine.01_03_BUSTER_model.cif.gz	including any non-standard compound restraints
5VYH_aB_refine.01_03_BUSTER_refln.cif.gz