Covid19Pdb5DO2

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:
    2.363         1.0000   0.0000   0.0000       a*
    2.493         0.0000   1.0000   0.0000       b*
    2.356         0.0000   0.0000   1.0000       c*

Deposited

Molprobity (CCP4 7.0 version) summary:

Ramachandran outliers =   0.79 %   
              favored =  95.15 %   
Rotamer outliers      =   5.01 %   
C-beta deviations     =     0   
Clashscore            =  13.44   
RMS(bonds)            =   0.0041   
RMS(angles)           =   0.95   
MolProbity score      =   2.51   
Resolution            =   2.41   
R-work                =   0.2450   
R-free                =   0.2890   

Additional analysis:

Number of waters      =   139

<B> (all atoms) =   73.88 ( sd =   39.11 ) for       9937 non-hydrogen atoms
<B>   (protein) =   74.08 ( sd =   39.33 ) for       9784 non-hydrogen atoms
<B>     (water) =   58.86 ( sd =   16.12 ) for        139 non-hydrogen atoms
<B>    (others) =   81.43 ( sd =    0.01 ) for         14 non-hydrogen atoms

B min/max       (all non-hydrogen atoms) =   25.10 /  246.29
B min/max   (protein non-hydrogen atoms) =   25.10 /  246.29
B min/max     (water non-hydrogen atoms) =   27.89 /   73.59
B min/max     (other non-hydrogen atoms) =   81.42 /   81.44

BUSTER (re-)refinement

Molprobity (CCP4 7.0 version) summary:

Ramachandran outliers =   0.56 %   
              favored =  96.82 %   
Rotamer outliers      =   5.80 %   
C-beta deviations     =     8   
Clashscore            =   4.36   
RMS(bonds)            =   0.0112   
RMS(angles)           =   1.63   
MolProbity score      =   1.99   
Resolution            =   2.41   
R-work                =   0.2227   
R-free                =   0.2576   

Additional analysis:

Number of waters      =   500

<B> (all atoms) =   72.74 ( sd =   36.96 ) for      10298 non-hydrogen atoms
<B>   (protein) =   73.75 ( sd =   37.51 ) for       9784 non-hydrogen atoms
<B>     (water) =   52.50 ( sd =   12.99 ) for        500 non-hydrogen atoms
<B>    (others) =   85.38 ( sd =    0.71 ) for         14 non-hydrogen atoms

B min/max       (all non-hydrogen atoms) =   22.96 /  193.06
B min/max   (protein non-hydrogen atoms) =   22.96 /  193.06
B min/max     (water non-hydrogen atoms) =   26.37 /  130.41
B min/max     (other non-hydrogen atoms) =   84.04 /   86.32

Refinement progression:

Results: