Resolution: 2.34→28.58 Å / Num. obs: 20155 / % possible obs: 99.6 % / Redundancy: 3.5 % / Rsym value: 0.088 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)
Redundancy (%)
Mean I/σ(I) obs
Num. measured obs
Rsym value
Diffraction-ID
% possible all
2.34-2.47
3.5
1.3
2891
0.583
1
99.8
2.47-2.62
3.6
1.7
2722
0.463
1
100
2.62-2.8
3.5
2.4
2593
0.321
1
99.9
2.8-3.02
3.5
3.4
2424
0.227
1
100
3.02-3.31
3.5
5.5
2243
0.14
1
99.9
3.31-3.7
3.5
9.6
2019
0.079
1
99.7
3.7-4.27
3.5
13.8
1819
0.05
1
99.7
4.27-5.23
3.5
17.5
1532
0.039
1
99.2
5.23-7.4
3.4
15.7
1216
0.045
1
98.3
7.4-28.58
3.1
22.4
696
0.027
1
94.6
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0005
refinement
SCALA
datascaling
PDB_EXTRACT
1.6
dataextraction
XDS
datareduction
CCP4
(SCALA)
datascaling
SHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.34→28.58 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.903 / SU B: 18.297 / SU ML: 0.203 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.24 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: OTHER REFINEMENT REMARKS: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2). ELECTRON DENSITY FOR PORTIONS OF THE N-TERMINAL DOMAIN IS QUITE POOR; THEREFORE, SEVERAL RESIDUES IN THIS ...Details: OTHER REFINEMENT REMARKS: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2). ELECTRON DENSITY FOR PORTIONS OF THE N-TERMINAL DOMAIN IS QUITE POOR; THEREFORE, SEVERAL RESIDUES IN THIS REGION COULD NOT BE MODELED. 3). ELECTRON DENSITIES FOR TWO SURFACE LOOPS BETWEEN RESIDUES 231-239 AND RESIDUES 294-297 ARE POOR. CONSEQUENTLY, THESE LOOPS WERE NOT MODELED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.275
1033
5.1 %
RANDOM
Rwork
0.221
-
-
-
all
0.223
-
-
-
obs
0.22326
19101
99.27 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 51.292 Å2
Baniso -1
Baniso -2
Baniso -3
1-
2.18 Å2
0 Å2
0 Å2
2-
-
2.18 Å2
0 Å2
3-
-
-
-4.36 Å2
Refinement step
Cycle: LAST / Resolution: 2.34→28.58 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2486
0
0
61
2547
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.013
0.022
2516
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
2287
X-RAY DIFFRACTION
r_angle_refined_deg
1.255
1.96
3398
X-RAY DIFFRACTION
r_angle_other_deg
0.74
3
5301
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.109
5
315
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.18
25.36
125
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.843
15
447
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.346
15
16
X-RAY DIFFRACTION
r_chiral_restr
0.068
0.2
390
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
2815
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
468
X-RAY DIFFRACTION
r_nbd_refined
0.206
0.2
540
X-RAY DIFFRACTION
r_nbd_other
0.173
0.2
2405
X-RAY DIFFRACTION
r_nbtor_refined
0.175
0.2
1236
X-RAY DIFFRACTION
r_nbtor_other
0.084
0.2
1633
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.114
0.2
79
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.172
0.2
7
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.162
0.2
46
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.114
0.2
9
X-RAY DIFFRACTION
r_mcbond_it
1.65
3
1650
X-RAY DIFFRACTION
r_mcbond_other
0.315
3
649
X-RAY DIFFRACTION
r_mcangle_it
2.592
5
2536
X-RAY DIFFRACTION
r_scbond_it
4.814
8
988
X-RAY DIFFRACTION
r_scangle_it
6.639
11
862
LS refinement shell
Resolution: 2.34→2.401 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.363
70
-
Rwork
0.3
1379
-
obs
-
-
99.38 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
3.6453
-3.0661
1.85
4.9089
-4.5348
15.0597
0.1057
0.1355
-0.2483
-0.2464
-0.0724
0.0864
1.1578
0.2245
-0.0334
-0.0565
-0.0558
0.0866
0.3333
-0.1272
0.1853
25.8679
40.0378
90.3676
2
2.2695
0.2705
2.398
1.9056
0.249
7.7041
0.1995
0.6711
-0.2114
-0.2614
0.0725
-0.1255
0.6626
0.5641
-0.272
-0.1871
0.0236
0.0392
-0.2401
-0.0453
-0.1267
58.0055
44.3855
74.9136
3
0.0516
0.1643
-0.1296
0.8362
1.1338
7.9665
-0.0038
0.1016
0.1187
-0.309
0.0322
0.0805
-0.2882
-0.2367
-0.0283
-0.1891
-0.0452
0.0001
-0.1963
0.0038
-0.0186
52.1119
48.4231
68.2666
Refinement TLS group
Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A
ID
Refine TLS-ID
Auth seq-ID
Label seq-ID
1
1
74 - 104
86 - 116
2
2
105 - 210
117 - 222
3
3
298 - 358
310 - 370
+
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