- PDB-2nlv: CRYSTAL STRUCTURE OF A XISI-LIKE PROTEIN (AVA_3825) FROM ANABAENA... -
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Basic information
Entry
Database: PDB / ID: 2nlv
Title
CRYSTAL STRUCTURE OF A XISI-LIKE PROTEIN (AVA_3825) FROM ANABAENA VARIABILIS ATCC 29413 AT 1.30 A RESOLUTION
Components
XisI protein-like
Keywords
UNKNOWN FUNCTION / XISI-LIKE PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2 / PSI-Biology
Function / homology
XisI-like / XisI protein / XisI-like superfamily / XisI protein / TATA-Binding Protein / 2-Layer Sandwich / Alpha Beta / XisI protein-like protein
Function and homology information
Biological species
Anabaena variabilis (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å
BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Resolution: 1.3→29.099 Å / Num. obs: 52812 / % possible obs: 98.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 7.9
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
1.3-1.33
3.6
0.618
1.2
13820
3797
0.618
96.3
1.33-1.37
3.6
0.516
1.4
13539
3742
0.516
97.8
1.37-1.41
3.6
0.419
1.8
13261
3666
0.419
97.7
1.41-1.45
3.6
0.348
2.1
12947
3560
0.348
97.5
1.45-1.5
3.6
0.267
2.8
12569
3468
0.267
97.7
1.5-1.55
3.6
0.222
3.3
12005
3329
0.222
98.1
1.55-1.61
3.6
0.174
4.2
11763
3266
0.174
98.9
1.61-1.68
3.6
0.143
5.1
11286
3140
0.143
98.8
1.68-1.75
3.6
0.117
6.2
10831
3016
0.117
98.9
1.75-1.84
3.6
0.092
7.8
10321
2892
0.092
99.1
1.84-1.94
3.6
0.095
6.6
9863
2772
0.095
99.4
1.94-2.06
3.5
0.062
10.4
9262
2615
0.062
99.5
2.06-2.2
3.5
0.055
11.8
8608
2473
0.055
99.5
2.2-2.37
3.2
0.063
8.5
6824
2137
0.063
93.1
2.37-2.6
3.2
0.046
12.7
6721
2111
0.046
98.9
2.6-2.91
3.5
0.042
14
6758
1912
0.042
99.9
2.91-3.36
3.7
0.037
14.3
6491
1734
0.037
100
3.36-4.11
3.7
0.029
19.8
5129
1394
0.029
97.1
4.11-5.81
3.7
0.026
20.9
4241
1146
0.026
100
5.81-29.1
3.5
0.029
15.1
2252
642
0.029
98.6
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
REFMAC
5.2.0019
refinement
SCALA
datascaling
PDB_EXTRACT
2
dataextraction
MOSFLM
datareduction
CCP4
(SCALA)
datascaling
SOLVE
phasing
RESOLVE
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.3→29.099 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.699 / SU ML: 0.037 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.056 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN ...Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (3) ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.195
2675
5.1 %
RANDOM
Rwork
0.175
-
-
-
obs
0.176
52745
98.13 %
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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: 9.824 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.01 Å2
0 Å2
0 Å2
2-
-
0.29 Å2
0 Å2
3-
-
-
-0.29 Å2
Refinement step
Cycle: LAST / Resolution: 1.3→29.099 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1808
0
4
296
2108
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.022
2117
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
1418
X-RAY DIFFRACTION
r_angle_refined_deg
1.758
1.948
2906
X-RAY DIFFRACTION
r_angle_other_deg
1
3
3467
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.642
5
273
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.736
24.455
110
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.956
15
385
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
21.174
15
17
X-RAY DIFFRACTION
r_chiral_restr
0.103
0.2
309
X-RAY DIFFRACTION
r_gen_planes_refined
0.01
0.02
2492
X-RAY DIFFRACTION
r_gen_planes_other
0.003
0.02
443
X-RAY DIFFRACTION
r_nbd_refined
0.239
0.2
387
X-RAY DIFFRACTION
r_nbd_other
0.206
0.2
1636
X-RAY DIFFRACTION
r_nbtor_refined
0.18
0.2
1058
X-RAY DIFFRACTION
r_nbtor_other
0.087
0.2
1171
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.193
0.2
197
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.39
0.2
15
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.31
0.2
32
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.151
0.2
27
X-RAY DIFFRACTION
r_mcbond_it
2.003
3
1389
X-RAY DIFFRACTION
r_mcbond_other
0.463
3
505
X-RAY DIFFRACTION
r_mcangle_it
2.48
5
2087
X-RAY DIFFRACTION
r_scbond_it
3.917
8
951
X-RAY DIFFRACTION
r_scangle_it
5.631
11
819
LS refinement shell
Resolution: 1.3→1.334 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.308
190
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Rwork
0.277
3600
-
obs
-
3790
96.27 %
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
0.4045
-0.181
0.1838
0.1259
-0.0779
0.1292
-0.0037
-0.0522
-0.0267
0.0178
0.0058
0.0234
0.0045
-0.048
-0.0021
-0.0027
-0.0086
0.0033
-0.0037
0.0034
-0.0065
34.1093
0.6239
13.238
2
0.7646
0.1877
0.0518
0.3875
0.5577
1.3614
-0.0038
-0.083
0.0009
-0.0499
0.0308
-0.022
-0.0229
0.2104
-0.027
-0.0213
-0.0111
0.0062
0.0123
-0.0012
-0.0182
54.1044
1.8808
18.764
Refinement TLS group
Refine-ID: X-RAY DIFFRACTION / Selection: ALL
ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
1
A
A
0 - 111
1 - 112
2
2
B
B
3 - 111
4 - 112
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