Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.979224
1
2
0.979508
1
3
0.885567
1
Reflection
Resolution: 2.67→29.928 Å / Num. obs: 34565 / % possible obs: 99.6 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.188 / Rsym value: 0.188 / Net I/σ(I): 3.7
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique obs
Rsym value
% possible all
2.67-2.74
5.8
0.892
0.8
14093
2426
0.892
96.5
2.74-2.81
6.6
0.769
1
16048
2425
0.769
99.3
2.81-2.9
7.7
0.67
1.1
18329
2374
0.67
99.9
2.9-2.99
10
0.582
1.3
23090
2317
0.582
100
2.99-3.08
10.6
0.516
1.5
24111
2269
0.516
100
3.08-3.19
10.6
0.376
2.1
23204
2184
0.376
100
3.19-3.31
10.6
0.312
2.5
22306
2110
0.312
100
3.31-3.45
10.5
0.237
1.8
21348
2027
0.237
100
3.45-3.6
10.5
0.188
4
20694
1972
0.188
100
3.6-3.78
10.4
0.149
5.1
19510
1869
0.149
100
3.78-3.98
10.4
0.136
5.5
18664
1787
0.136
100
3.98-4.22
10.4
0.121
6.3
17635
1702
0.121
100
4.22-4.51
10.3
0.096
7.7
16530
1606
0.096
99.7
4.51-4.87
10.2
0.101
7.2
15260
1499
0.101
100
4.87-5.34
10
0.125
5.7
13941
1395
0.125
100
5.34-5.97
9.8
0.165
4.3
12358
1264
0.165
100
5.97-6.89
9.6
0.136
5.3
10989
1147
0.136
100
6.89-8.44
8.8
0.08
8.5
8540
965
0.08
99.5
8.44-11.94
9.5
0.056
11.7
7479
785
0.056
99.9
11.94-29.93
8.6
0.059
10.8
3805
442
0.059
93.7
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0005
refinement
SCALA
datascaling
PDB_EXTRACT
1.701
dataextraction
MOSFLM
datareduction
CCP4
(SCALA)
datascaling
SOLVE
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.67→29.57 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.892 / SU B: 16.895 / SU ML: 0.175 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.388 / ESU R Free: 0.262 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THERE ARE TWO RAMACHANDRAN OUTLIERS, WHICH ARE SUPPORTED BY THE DENSITY. 3. PHOSPHATE IS MODELED INTO THE PUTATIVE ADP BINDING SITE. ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THERE ARE TWO RAMACHANDRAN OUTLIERS, WHICH ARE SUPPORTED BY THE DENSITY. 3. PHOSPHATE IS MODELED INTO THE PUTATIVE ADP BINDING SITE. 4. FORMATE AND ETHYLENE GLYCOL MODELED BASED ON CRYSTALLIZATION CONDITIONS. 5. RESIDUES A117-118 ARE DISORDERED AND WERE NOT MODELED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.238
1734
5 %
RANDOM
Rwork
0.207
-
-
-
obs
0.208
34472
99.56 %
-
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: 32.967 Å2
Refinement step
Cycle: LAST / Resolution: 2.67→29.57 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5176
0
25
148
5349
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.022
5330
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
5011
X-RAY DIFFRACTION
r_angle_refined_deg
2.367
1.974
7230
X-RAY DIFFRACTION
r_angle_other_deg
1.482
3
11619
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
1.897
5
679
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
29.912
23.953
215
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
9.58
15
896
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
11.515
15
29
X-RAY DIFFRACTION
r_chiral_restr
0.1
0.2
826
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
5899
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
1046
X-RAY DIFFRACTION
r_nbd_refined
0.205
0.2
991
X-RAY DIFFRACTION
r_nbd_other
0.153
0.2
4996
X-RAY DIFFRACTION
r_nbtor_refined
0.172
0.2
2645
X-RAY DIFFRACTION
r_nbtor_other
0.08
0.2
3141
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.139
0.2
166
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.011
0.2
1
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.146
0.2
21
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.212
0.2
43
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.046
0.2
8
X-RAY DIFFRACTION
r_mcbond_it
0.537
1.5
3652
X-RAY DIFFRACTION
r_mcbond_other
0.078
1.5
1394
X-RAY DIFFRACTION
r_mcangle_it
0.738
2
5413
X-RAY DIFFRACTION
r_scbond_it
0.927
3
2157
X-RAY DIFFRACTION
r_scangle_it
1.454
4.5
1814
Refine LS restraints NCS
Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION
Ens-ID
Number
Type
Rms dev position (Å)
Weight position
1
591
TIGHTPOSITIONAL
0.03
0.05
1
894
MEDIUMPOSITIONAL
0.35
0.5
1
591
TIGHTTHERMAL
0.06
0.5
1
894
MEDIUMTHERMAL
0.21
2
2
130
TIGHTPOSITIONAL
0.02
0.05
2
190
MEDIUMPOSITIONAL
0.32
0.5
2
130
TIGHTTHERMAL
0.09
0.5
2
190
MEDIUMTHERMAL
0.15
2
3
526
TIGHTPOSITIONAL
0.06
0.05
3
792
MEDIUMPOSITIONAL
0.4
0.5
3
526
TIGHTTHERMAL
0.06
0.5
3
792
MEDIUMTHERMAL
0.23
2
4
209
TIGHTPOSITIONAL
0.03
0.05
4
324
MEDIUMPOSITIONAL
0.1
0.5
4
209
TIGHTTHERMAL
0.05
0.5
4
324
MEDIUMTHERMAL
0.21
2
5
210
TIGHTPOSITIONAL
0.05
0.05
5
293
MEDIUMPOSITIONAL
0.42
0.5
5
210
TIGHTTHERMAL
0.09
0.5
5
293
MEDIUMTHERMAL
0.3
2
LS refinement shell
Resolution: 2.671→2.74 Å / Total num. of bins used: 20
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