Covid19Pdb2AMD

Content:

• See also
• Deposited
• (Re-)refinement

See also:

• RCSB
• PDBe
• PDBj

• PDB-REDO

• PDBpeep

    Diffraction limits & principal axes of ellipsoid fitted to diffraction cut-off surface:
    1.856         0.8980   0.0000   0.4399       0.951 a* + 0.309 c*
    1.831         0.0000   1.0000   0.0000       b*
    1.823        -0.4399   0.0000   0.8980      -0.329 a* + 0.944 c*

Deposited

Molprobity (CCP4 7.0 version) summary:

Ramachandran outliers =   0.49 %   
              favored =  97.54 %   
Rotamer outliers      =   3.81 %   
C-beta deviations     =     0   
Clashscore            =  12.98   
RMS(bonds)            =   0.0062   
RMS(angles)           =   1.42   
MolProbity score      =   2.16   
Resolution            =   1.85   
R-work                =   0.2150   
R-free                =   0.2450   

Additional analysis:

Number of waters      =   401

<B> (all atoms) =   28.93 ( sd =    8.62 ) for       5223 non-hydrogen atoms
<B>   (protein) =   28.20 ( sd =    8.35 ) for       4732 non-hydrogen atoms
<B>     (water) =   36.84 ( sd =    7.94 ) for        401 non-hydrogen atoms
<B>    (others) =   32.24 ( sd =    7.15 ) for         90 non-hydrogen atoms

B min/max       (all non-hydrogen atoms) =   15.65 /   65.77
B min/max   (protein non-hydrogen atoms) =   15.65 /   65.77
B min/max     (water non-hydrogen atoms) =   18.67 /   60.80
B min/max     (other non-hydrogen atoms) =   23.00 /   53.28

BUSTER (re-)refinement

Molprobity (CCP4 7.0 version) summary:

Ramachandran outliers =   0.33 %   
              favored =  97.87 %   
Rotamer outliers      =   4.38 %   
C-beta deviations     =     2   
Clashscore            =   5.65   
RMS(bonds)            =   0.0122   
RMS(angles)           =   1.58   
MolProbity score      =   1.83   
Resolution            =   1.86   
R-work                =   0.1963   
R-free                =   0.2276   

Additional analysis:

Number of waters      =   483

<B> (all atoms) =   29.76 ( sd =    9.32 ) for       5305 non-hydrogen atoms
<B>   (protein) =   28.72 ( sd =    8.67 ) for       4732 non-hydrogen atoms
<B>     (water) =   39.88 ( sd =    9.93 ) for        483 non-hydrogen atoms
<B>    (others) =   30.20 ( sd =    5.58 ) for         90 non-hydrogen atoms

B min/max       (all non-hydrogen atoms) =   16.86 /   77.41
B min/max   (protein non-hydrogen atoms) =   16.86 /   77.41
B min/max     (water non-hydrogen atoms) =   18.34 /   72.17
B min/max     (other non-hydrogen atoms) =   23.98 /   46.75

Refinement progression:

Results: