Resolution: 0.96→0.99 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.32 / Num. unique all: 26836 / Rsym value: 0.375 / % possible all: 91.7
-
Processing
Software
Name
Version
Classification
REFMAC
5.2.0019
refinement
PF
native
datacollection
DENZO
datareduction
SCALEPACK
datascaling
SHELXE
modelbuilding
Refinement
Method to determine structure: MAD / Resolution: 0.96→20 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.408 / SU ML: 0.011 / Cross valid method: THROUGHOUT / ESU R: 0.018 / ESU R Free: 0.019 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The position of the CB atom of Thr426 must be correct in the electron density map. And The author beleives that the 2fo-fc electron density ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The position of the CB atom of Thr426 must be correct in the electron density map. And The author beleives that the 2fo-fc electron density map and the model fit well with each other and reliable because of the resolution 0.96A and the free R value.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.14606
14789
5.1 %
RANDOM
Rwork
0.13264
-
-
-
obs
0.13332
277615
100 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 9.397 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.07 Å2
0 Å2
0 Å2
2-
-
-0.14 Å2
0 Å2
3-
-
-
0.21 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.1999 Å
0.1969 Å
Luzzati d res low
-
5 Å
Luzzati sigma a
0.0567 Å
0.0388 Å
Refinement step
Cycle: LAST / Resolution: 0.96→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4012
0
27
574
4613
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
4243
X-RAY DIFFRACTION
r_angle_refined_deg
1.788
1.953
5779
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.166
5
508
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.121
24.856
208
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.878
15
731
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
10.82
15
17
X-RAY DIFFRACTION
r_chiral_restr
0.225
0.2
602
X-RAY DIFFRACTION
r_gen_planes_refined
0.013
0.02
3279
X-RAY DIFFRACTION
r_nbd_refined
0.212
0.2
2024
X-RAY DIFFRACTION
r_nbtor_refined
0.318
0.2
2961
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.112
0.2
472
X-RAY DIFFRACTION
r_metal_ion_refined
0.064
0.2
8
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.138
0.2
51
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.075
0.2
23
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
0.032
0.2
1
X-RAY DIFFRACTION
r_mcbond_it
1.452
1.5
2564
X-RAY DIFFRACTION
r_mcangle_it
2.032
2
4115
X-RAY DIFFRACTION
r_scbond_it
2.907
3
1928
X-RAY DIFFRACTION
r_scangle_it
3.859
4.5
1644
X-RAY DIFFRACTION
r_rigid_bond_restr
1.514
3
4492
X-RAY DIFFRACTION
r_sphericity_free
9.999
3
577
X-RAY DIFFRACTION
r_sphericity_bonded
3.843
3
4121
LS refinement shell
Resolution: 0.96→0.985 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.295
1027
-
Rwork
0.272
18219
-
obs
-
-
100 %
+
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