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
0.885567
1
2
0.976224
1
Reflection
Resolution: 2.4→29.2 Å / Num. obs: 31322 / % possible obs: 99.5 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 5.9
Reflection shell
Resolution: 2.46→2.52 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.633 / Mean I/σ(I) obs: 1.2 / Rsym value: 0.633 / % possible all: 95
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
SCALA
datascaling
PDB_EXTRACT
1.601
dataextraction
MOSFLM
datareduction
CCP4
(SCALA)
datascaling
SnB
phasing
MLPHARE
phasing
SOLVE
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.46→28.49 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / SU B: 16.907 / SU ML: 0.177 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.355 / ESU R Free: 0.248 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. UNMODELED DENSITY NEAR A234.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24
1595
5.1 %
RANDOM
Rwork
0.193
-
-
-
obs
-
29692
99.4 %
-
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: 31.77 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.31 Å2
0 Å2
0 Å2
2-
-
1.31 Å2
0 Å2
3-
-
-
-2.62 Å2
Refinement step
Cycle: LAST / Resolution: 2.46→28.49 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5013
0
10
42
5065
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.012
0.022
5123
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
3487
X-RAY DIFFRACTION
r_angle_refined_deg
1.274
1.972
6930
X-RAY DIFFRACTION
r_angle_other_deg
0.825
3
8518
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.194
5
642
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.829
23.991
223
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.005
15
912
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.688
15
33
X-RAY DIFFRACTION
r_chiral_restr
0.073
0.2
796
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.02
5669
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
1034
X-RAY DIFFRACTION
r_nbd_refined
0.204
0.2
975
X-RAY DIFFRACTION
r_nbd_other
0.183
0.2
3440
X-RAY DIFFRACTION
r_nbtor_refined
0.181
0.2
2529
X-RAY DIFFRACTION
r_nbtor_other
0.086
0.2
2849
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.148
0.2
110
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.158
0.2
15
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.204
0.2
63
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.159
0.2
7
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
1.719
3
3405
X-RAY DIFFRACTION
r_mcbond_other
0.391
3
1302
X-RAY DIFFRACTION
r_mcangle_it
2.525
5
5170
X-RAY DIFFRACTION
r_scbond_it
5.131
8
2107
X-RAY DIFFRACTION
r_scangle_it
6.864
11
1758
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
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
149
mediumpositional
0.22
0.5
2
417
mediumpositional
0.17
0.5
3
1217
mediumpositional
0.18
0.5
1
195
loosepositional
0.68
5
2
479
loosepositional
0.53
5
3
1506
loosepositional
0.68
5
1
149
mediumthermal
0.69
2
2
417
mediumthermal
0.73
2
3
1217
mediumthermal
0.67
2
1
195
loosethermal
1.71
10
2
479
loosethermal
2.1
10
3
1506
loosethermal
2.11
10
LS refinement shell
Resolution: 2.46→2.52 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.414
108
-
Rwork
0.322
2038
-
obs
-
-
94.83 %
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
1.7141
-0.5293
0.7834
1.3932
-1.0642
2.2321
0.201
-0.1742
0.0252
-0.0217
0.0686
0.1388
0.2144
-0.4228
-0.2696
-0.0879
-0.0031
0.0102
-0.0611
0.0245
-0.108
35.047
4.139
111.925
2
1.9358
1.2468
0.4488
2.5841
-0.0083
1.3323
0.2444
-0.1933
-0.0318
0.3965
-0.2725
0.0122
-0.0761
0.0694
0.0281
-0.0231
-0.0862
0.0256
-0.0309
0.0201
-0.1343
69.869
19.856
132.441
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
X-RAY DIFFRACTION
1
A
A
0 - 319
12 - 331
2
X-RAY DIFFRACTION
2
B
B
0 - 319
12 - 331
+
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