Please also check the autoPROC (Re)processing page for 6W9C



The 6W9C model was solved via molecular replacement (with Phaser) using 5Y3Q and refined in REFMAC.

Deposited model and data

Given the low completeness (see remarks on autoPROC (re)processing page), it is not surprising that the overall validation metrics are on the slightly poorer side. here are some numbers with different versions of the MolProbity suite/method:

MolProbity 4.02:

    |        |Clashscore, all atoms:|6.57           |99th percentile* (N=189,   |
    |Contacts|Clashscore is the number of serious steric overlaps (> 0.4 AA) per|
    |        |Poor_rotamers_________|40______|4.93%_|Goal:_<1%__________________|
    |        |Ramachandran_outliers_|5_______|0.54%_|Goal:_<0.05%_______________|
    |        |Ramachandran_favored__|779_____|84.40%|Goal:_>98%_________________|
    |Protein |MolProbity score^     |2.56           |83rd percentile* (N=5412,  |
    |        |Cb_deviations_>0.25AA_|0_______|0.00%_|Goal:_0____________________|
    |        |Bad_backbone_bonds:___|0_/_3720|0.00%_|Goal:_0%___________________|

CCTBX version (as distributed with CCP4):

     Ramachandran outliers =   0.54 %   
                   favored =  84.40 %   
     Rotamer outliers      =   7.39 %   
     C-beta deviations     =     0   
     Clashscore            =   6.70 (percentile: 64.1 N=23192, 2.70A+/-0.25A) 
     RMS(bonds)            =   0.0135   
     RMS(angles)           =   1.77   
     MolProbity score      =   2.70 (percentile: 33.2 N=22793, 2.70A+/-0.25A) 
     Resolution            =   2.70   
     R-work                =   0.2350 (percentile: 17.4 N=23083, 2.70A+/-0.25A) 
     R-free                =   0.3090 (percentile: 5.5 N=22111, 2.70A+/-0.25A) 
     Refinement program    = REFMAC 

(Re)processed data and refinement

We will be using the re-processed data and start again from an initial "MR-like" starting point. For that we are

The idea is to start with a good geometry model (since 5Y3Q is a 1.65 A structure with complete data and good validation metrics. So what can be done from this starting point: