- PDB-3gby: Crystal structure of a protein with unknown function CT1051 from ... -
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Basic information
Entry
Database: PDB / ID: 3gby
Title
Crystal structure of a protein with unknown function CT1051 from Chlorobium tepidum
Components
Uncharacterized protein CT1051
Keywords
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Chlorobium tepidum / CBS domain / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
CBS-domain / CBS-domain / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta / Uncharacterized protein
Function and homology information
Biological species
Chlorobium tepidum TLS (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.66 Å
Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97937 Å / Relative weight: 1
Reflection
Resolution: 1.66→50 Å / Num. all: 27829 / Num. obs: 27379 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 43.8
Reflection shell
Resolution: 1.66→1.67 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.826 / Mean I/σ(I) obs: 1.9 / Num. unique all: 425 / % possible all: 59.4
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Processing
Software
Name
Version
Classification
SBC-Collect
datacollection
HKL-3000
phasing
SHELXD
phasing
SHELXE
modelbuilding
MLPHARE
phasing
DM
modelbuilding
RESOLVE
modelbuilding
REFMAC
5.5.0054
refinement
HKL-3000
datareduction
HKL-3000
datascaling
DM
phasing
RESOLVE
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.66→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.967 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.206 / ESU R Free: 0.115 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22632
1357
5 %
RANDOM
Rwork
0.17929
-
-
-
all
0.1818
26597
-
-
obs
0.1818
26597
97.43 %
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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: 17.659 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.04 Å2
0 Å2
-0.76 Å2
2-
-
1.02 Å2
0 Å2
3-
-
-
-0.11 Å2
Refinement step
Cycle: LAST / Resolution: 1.66→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1995
0
40
249
2284
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.016
0.022
2076
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.545
2.003
2825
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.413
5
270
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.488
22.184
87
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.554
15
341
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.506
15
23
X-RAY DIFFRACTION
r_chiral_restr
0.09
0.2
314
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.021
1559
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
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
1.244
1.5
1299
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
2.049
2
2082
X-RAY DIFFRACTION
r_scbond_it
3.176
3
777
X-RAY DIFFRACTION
r_scangle_it
4.873
4.5
740
X-RAY DIFFRACTION
r_rigid_bond_restr
1.858
3
2076
X-RAY DIFFRACTION
r_sphericity_free
5.772
3
249
X-RAY DIFFRACTION
r_sphericity_bonded
2.624
3
2035
LS refinement shell
Resolution: 1.66→1.71 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.338
81
-
Rwork
0.275
1632
-
obs
-
1713
84.93 %
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
2.2306
-0.1748
0.5167
0.7004
-0.5169
2.2869
0.0231
0.1088
-0.0018
-0.0117
0.0442
0.0828
0.0192
-0.0794
-0.0673
0.1524
0
0.0202
0.1128
0.0048
0.0184
22.424
9.729
4.145
2
3.6114
0.6984
0.5296
1.4839
0.3521
1.7075
0.0744
0.1485
-0.0493
0.0076
0.0211
-0.1857
0.0295
0.2969
-0.0955
0.1551
0.0235
0.0292
0.2013
-0.024
0.0375
43.425
5.294
6.34
3
1.9111
0.4125
-0.8272
1.2277
-0.0823
2.4235
-0.0056
-0.1466
0.0158
0.0343
0.0448
0.1078
-0.0014
-0.0818
-0.0393
0.1383
0.0125
0.0275
0.1641
0.0066
0.0169
20.338
9.073
25.96
4
2.2182
-1.5283
-2.6019
2.4974
2.9707
5.8063
-0.0544
-0.8206
0.2341
0.1355
0.6515
-0.4286
0.173
1.4006
-0.5971
0.1483
0.0123
-0.0039
0.5518
-0.1569
0.0937
41.153
13.108
27.969
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
-1 - 12
2
X-RAY DIFFRACTION
1
A
76 - 125
3
X-RAY DIFFRACTION
2
A
13 - 75
4
X-RAY DIFFRACTION
3
B
-1 - 12
5
X-RAY DIFFRACTION
3
B
76 - 125
6
X-RAY DIFFRACTION
4
B
13 - 75
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