Method to determine structure: MAD / Resolution: 2.491→45.27 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.28 / Stereochemistry target values: ML Details: The authors performed MAD experiment with Potassium tetra nitro Platinate as heavy atom complex using the wavelengths 1.07155(peak), 1.07182(inflection) and 1.06878(remote). The data was ...Details: The authors performed MAD experiment with Potassium tetra nitro Platinate as heavy atom complex using the wavelengths 1.07155(peak), 1.07182(inflection) and 1.06878(remote). The data was uploaded to the autorickshaw server (http://www.embl-hamburg.de/Auto-Rickshaw/) and then used the biggest fragment with the best e-density fit of the resulting model to do Molecular replacement into a nativ data set with higher resolution. After this, the model building process was done manually using phenix.autobuild. The data in the session are for the native data set. So the phasing method was a mixture of MR and MAD.
Rfactor
Num. reflection
% reflection
Rfree
0.224
2498
5.09 %
Rwork
0.1883
-
-
obs
0.1901
49067
98.1 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 2.491→45.27 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
9909
0
15
408
10332
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.005
10192
X-RAY DIFFRACTION
f_angle_d
0.771
13758
X-RAY DIFFRACTION
f_dihedral_angle_d
12.958
3781
X-RAY DIFFRACTION
f_chiral_restr
0.04
1415
X-RAY DIFFRACTION
f_plane_restr
0.003
1792
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.4915-2.5394
0.3369
131
0.2782
2229
X-RAY DIFFRACTION
87
2.5394-2.5912
0.3231
129
0.261
2587
X-RAY DIFFRACTION
98
2.5912-2.6475
0.3115
149
0.2533
2564
X-RAY DIFFRACTION
99
2.6475-2.7091
0.2682
139
0.2431
2557
X-RAY DIFFRACTION
99
2.7091-2.7769
0.3178
131
0.2495
2589
X-RAY DIFFRACTION
99
2.7769-2.8519
0.2637
152
0.2412
2571
X-RAY DIFFRACTION
99
2.8519-2.9358
0.2873
139
0.2375
2562
X-RAY DIFFRACTION
99
2.9358-3.0306
0.3097
130
0.2362
2591
X-RAY DIFFRACTION
99
3.0306-3.1389
0.2389
131
0.2186
2584
X-RAY DIFFRACTION
99
3.1389-3.2645
0.2798
137
0.2139
2604
X-RAY DIFFRACTION
99
3.2645-3.413
0.248
134
0.2066
2613
X-RAY DIFFRACTION
99
3.413-3.5929
0.2364
134
0.1979
2609
X-RAY DIFFRACTION
99
3.5929-3.8179
0.2006
139
0.1826
2636
X-RAY DIFFRACTION
99
3.8179-4.1125
0.1836
157
0.1644
2591
X-RAY DIFFRACTION
99
4.1125-4.526
0.1801
130
0.1437
2661
X-RAY DIFFRACTION
99
4.526-5.1801
0.1786
156
0.1409
2627
X-RAY DIFFRACTION
99
5.1801-6.5233
0.1782
144
0.1584
2687
X-RAY DIFFRACTION
99
6.5233-45.2776
0.1745
136
0.1487
2707
X-RAY DIFFRACTION
95
+
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