Group: Advisory / Source and taxonomy / Version format compliance
Remark 300
BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL MOLECULE FOR THE PROTEIN IS NOT KNOWN.
Resolution: 2.35→2.41 Å / Redundancy: 18.9 % / Rmerge(I) obs: 0.894 / Mean I/σ(I) obs: 4.1 / % possible all: 99.6
-
Processing
Software
Name
Version
Classification
REFMAC
5.2.0005
refinement
HKL-2000
datareduction
SCALEPACK
datascaling
SHELXD
phasing
SOLVE
phasing
RESOLVE
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.35→40 Å / Cor.coef. Fo:Fc: 0.944 / SU B: 8.742 / SU ML: 0.107 / TLS residual ADP flag: LIKELY RESIDUAL / σ(F): 0 / σ(I): 0 / ESU R: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, ALL DATA WERE USED IN FINAL ROUND OF REFINEMENT. R-FACTOR-ALL CORRESPONDS TO DEPOSITED FILE. R-WORK AND R-FREE FACTORS ARE TAKEN FROM ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, ALL DATA WERE USED IN FINAL ROUND OF REFINEMENT. R-FACTOR-ALL CORRESPONDS TO DEPOSITED FILE. R-WORK AND R-FREE FACTORS ARE TAKEN FROM SECOND TO LAST ROUND OF REFINEMENT WHICH USED TEST DATA SET. MLY RESIDUE CORRESPONDS TO N-DIMETHYL-LYSINE (C8 H18 N2 O2)
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2439
1450
-
RANDOM
Rwork
0.201
-
-
-
all
0.1998
14465
-
-
obs
0.1998
14465
99.8 %
-
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: 46.014 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.17 Å2
0 Å2
0 Å2
2-
-
1.17 Å2
0 Å2
3-
-
-
-2.34 Å2
Refinement step
Cycle: LAST / Resolution: 2.35→40 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1803
0
2
74
1879
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.021
1851
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.654
1.988
2510
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.38
5
224
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.808
23.371
89
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
18.086
15
302
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.176
15
19
X-RAY DIFFRACTION
r_chiral_restr
0.118
0.2
287
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
1391
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.217
0.2
862
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.303
0.2
1252
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.167
0.2
82
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
0.179
0.2
39
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.24
0.2
4
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
1.127
1.5
1172
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.813
2
1820
X-RAY DIFFRACTION
r_scbond_it
2.984
3
773
X-RAY DIFFRACTION
r_scangle_it
4.638
4.5
690
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.353→2.414 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.276
97
-
Rwork
0.219
1019
-
obs
-
1019
98.08 %
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
3.4358
-1.312
-0.3181
0.7569
0.0483
0.9786
0.1171
0.0882
-0.2258
-0.0646
0.0075
0.0465
0.1431
0.29
-0.1246
-0.0276
0.0908
-0.0245
-0.01
-0.0186
-0.1115
13.637
28.0521
34.6926
2
2.2776
-0.5382
0.5752
0.5762
0.1062
1.5913
0.084
-0.0282
-0.0557
-0.1265
0.0634
0.0659
-0.0608
-0.0224
-0.1473
-0.0164
0.0062
0.0021
-0.0299
0.0165
-0.0839
-3.5998
36.9135
34.6293
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
9 - 122
12 - 125
2
X-RAY DIFFRACTION
2
B
B
12 - 123
15 - 126
+
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