- PDB-3g1c: The crystal structure of a TrpR like protein from Eubacterium eli... -
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Open data
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Basic information
Entry
Database: PDB / ID: 3g1c
Title
The crystal structure of a TrpR like protein from Eubacterium eligens ATCC 27750
Components
The TrpR like protein from Eubacterium eligens ATCC 27750
Keywords
transcription / DNA binding protein / TrpR like protein / Eubacterium eligens / Structural Genomics / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics / unknown function
Resolution: 2.2→2.257 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 1.28 / Num. unique all: 594 / % possible all: 94.44
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Processing
Software
Name
Version
Classification
SBC-Collect
datacollection
HKL-3000
phasing
REFMAC
5.5.0054
refinement
HKL-3000
datareduction
HKL-3000
datascaling
Refinement
Method to determine structure: SAD / Resolution: 2.2→38.63 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.544 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1.28 / ESU R: 0.2 / ESU R Free: 0.174 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23657
381
4.6 %
RANDOM
Rwork
0.20484
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-
-
obs
0.20632
7885
99.24 %
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all
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7945
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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: 39.638 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.72 Å2
0 Å2
0 Å2
2-
-
1.72 Å2
0 Å2
3-
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-3.44 Å2
Refinement step
Cycle: LAST / Resolution: 2.2→38.63 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
787
0
3
59
849
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.022
0.022
796
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
547
X-RAY DIFFRACTION
r_angle_refined_deg
1.6
1.965
1069
X-RAY DIFFRACTION
r_angle_other_deg
0.901
3
1327
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.673
5
96
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.954
24.419
43
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.496
15
152
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
23.461
15
7
X-RAY DIFFRACTION
r_chiral_restr
0.103
0.2
121
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.02
884
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
167
X-RAY DIFFRACTION
r_mcbond_it
1.099
1.5
480
X-RAY DIFFRACTION
r_mcbond_other
0.253
1.5
197
X-RAY DIFFRACTION
r_mcangle_it
2.186
2
770
X-RAY DIFFRACTION
r_scbond_it
3.336
3
316
X-RAY DIFFRACTION
r_scangle_it
5.608
4.5
299
LS refinement shell
Resolution: 2.2→2.257 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.296
29
-
Rwork
0.245
532
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obs
-
561
94.44 %
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