Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9794 Å / Relative weight: 1
Reflection
Resolution: 2.6→50 Å / Num. all: 19411 / Num. obs: 19380 / % possible obs: 99.84 % / Observed criterion σ(I): 2 / Redundancy: 14.5 % / Biso Wilson estimate: 50.1 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 28.57
Reflection shell
Resolution: 2.6→2.668 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2 / % possible all: 98.61
-
Processing
Software
Name
Version
Classification
REFMAC
5.2.0019
refinement
SBC-Collect
datacollection
HKL-3000
datareduction
HKL-3000
datascaling
HKL-3000
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.6→48.17 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.906 / SU B: 19.317 / SU ML: 0.203 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.332 / ESU R Free: 0.267 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The N-terminal of Mol.A (residues 73-86) and Mol.B (residues 73-88) can not be refined very well due to the lack of the density of the sidechains.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.27002
1038
5.1 %
RANDOM
Rwork
0.22361
-
-
-
obs
0.22595
19380
99.84 %
-
all
-
19380
-
-
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: 50.097 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.08 Å2
-0.04 Å2
0 Å2
2-
-
-0.08 Å2
0 Å2
3-
-
-
0.12 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.045 Å
0.042 Å
Luzzati d res low
-
6 Å
Luzzati sigma a
0.5 Å
0.41 Å
Refinement step
Cycle: LAST / Resolution: 2.6→48.17 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2592
0
2
49
2643
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.016
0.022
2704
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1853
X-RAY DIFFRACTION
r_angle_refined_deg
1.798
1.955
3647
X-RAY DIFFRACTION
r_angle_other_deg
1.074
3
4500
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
8.427
5
318
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.737
23.897
136
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
20.206
15
480
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
22.496
15
14
X-RAY DIFFRACTION
r_chiral_restr
0.116
0.2
395
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
2971
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
587
X-RAY DIFFRACTION
r_nbd_refined
0.237
0.2
580
X-RAY DIFFRACTION
r_nbd_other
0.205
0.2
1992
X-RAY DIFFRACTION
r_nbtor_refined
0.197
0.2
1246
X-RAY DIFFRACTION
r_nbtor_other
0.091
0.2
1542
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.204
0.2
93
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.166
0.2
1
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.144
0.2
12
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.195
0.2
15
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.071
0.2
2
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
1.011
1.5
2040
X-RAY DIFFRACTION
r_mcbond_other
0.119
1.5
642
X-RAY DIFFRACTION
r_mcangle_it
1.203
2
2598
X-RAY DIFFRACTION
r_scbond_it
1.615
3
1310
X-RAY DIFFRACTION
r_scangle_it
2.411
4.5
1049
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.6→2.668 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.381
67
-
Rwork
0.336
1422
-
obs
-
-
98.61 %
Refinement TLS params.
Method: refined / Origin x: 19.811 Å / Origin y: 44.744 Å / Origin z: 57.401 Å
11
12
13
21
22
23
31
32
33
T
0.1201 Å2
0.1106 Å2
-0.009 Å2
-
0.1793 Å2
-0.0092 Å2
-
-
-0.0402 Å2
L
1.1385 °2
-0.2523 °2
1.5851 °2
-
0.2805 °2
-0.7105 °2
-
-
3.2025 °2
S
0.083 Å °
-0.1248 Å °
-0.1777 Å °
0.0195 Å °
0.0793 Å °
0.1004 Å °
0.1184 Å °
-0.2299 Å °
-0.1623 Å °
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
73 - 91
1 - 19
2
X-RAY DIFFRACTION
1
A
A
92 - 140
20 - 68
3
X-RAY DIFFRACTION
1
A
A
141 - 180
69 - 108
4
X-RAY DIFFRACTION
1
A
A
181 - 233
109 - 161
5
X-RAY DIFFRACTION
1
B
B
73 - 91
1 - 19
6
X-RAY DIFFRACTION
1
B
B
92 - 140
20 - 68
7
X-RAY DIFFRACTION
1
B
B
141 - 180
69 - 108
8
X-RAY DIFFRACTION
1
B
B
181 - 233
109 - 161
+
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