Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 600
HETEROGEN Residues H30, H32, W366, D397 coordinate a putative metal ion which has been modeled as ...HETEROGEN Residues H30, H32, W366, D397 coordinate a putative metal ion which has been modeled as water 1 (chain A), 2 (chain B) and 3 (chain C).'
Resolution: 2.85→76.7 Å / Num. obs: 38502 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 19.36 Å2 / Rsym value: 0.075 / Net I/σ(I): 5.2
Reflection shell
Resolution: 2.85→2.95 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.232 / % possible all: 96.1
-
Processing
Software
Name
Version
Classification
MOSFLM
datareduction
SCALA
datascaling
CCP4
datareduction
CCP4
modelbuilding
SOLVE
phasing
RESOLVE
modelbuilding
REFMAC
5
refinement
CCP4
(SCALA)
datascaling
CCP4
phasing
RESOLVE
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.85→24.99 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.831 / SU B: 21.087 / SU ML: 0.419 / Cross valid method: THROUGHOUT / ESU R Free: 0.439 Details: HOMOTRIMER, INVISIBLE SIDECHAIN IN RESIDUES 12,36,112,128,168,178,185,187,190,191,194,195,222, 223,257,258,398, UNACCOUNTED DENSITY NEXT TO M377 AND P344, UNACCOUNTED DENSITY NEXT TO R178.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.274
1938
5 %
RANDOM
Rwork
0.234
-
-
-
obs
-
36521
96.6 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 31.307 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.01 Å2
-0.71 Å2
-0.4 Å2
2-
-
-0.34 Å2
0.01 Å2
3-
-
-
-0.27 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.34 Å
0.36 Å
Luzzati d res low
-
6 Å
Refinement step
Cycle: LAST / Resolution: 2.85→24.99 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
11068
0
0
107
11175
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.02
0.021
11122
X-RAY DIFFRACTION
r_bond_other_d
0.003
0.02
9907
X-RAY DIFFRACTION
r_angle_refined_deg
1.676
1.936
15100
X-RAY DIFFRACTION
r_angle_other_deg
0.937
3
22954
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.139
3
1348
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
19.291
15
1959
X-RAY DIFFRACTION
r_chiral_restr
0.095
0.2
1628
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
12389
X-RAY DIFFRACTION
r_gen_planes_other
0.003
0.02
2361
X-RAY DIFFRACTION
r_nbd_refined
0.271
0.3
3297
X-RAY DIFFRACTION
r_nbd_other
0.248
0.3
11132
X-RAY DIFFRACTION
r_nbtor_other
0.03
0.5
5
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.231
0.5
1012
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.148
0.5
38
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.511
0.3
37
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.474
0.3
41
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.496
0.5
8
X-RAY DIFFRACTION
r_symmetry_hbond_other
0.395
0.5
1
X-RAY DIFFRACTION
r_mcbond_it
1.285
2
6723
X-RAY DIFFRACTION
r_mcangle_it
2.291
3
10820
X-RAY DIFFRACTION
r_scbond_it
1.069
2
4399
X-RAY DIFFRACTION
r_scangle_it
1.823
3
4280
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.85→2.92 Å / Total num. of bins used: 20 /
Rfactor
Num. reflection
Rfree
0.331
162
Rwork
0.265
2704
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rwork: 0.233
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
r_bond_d
0.02
X-RAY DIFFRACTION
r_angle_d
X-RAY DIFFRACTION
r_angle_deg
1.67
+
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