- PDB-3fyf: Crystal structure of uncharacterized protein bvu_3222 from bacter... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3fyf
Title
Crystal structure of uncharacterized protein bvu_3222 from bacteroides vulgatus
Components
PROTEIN BVU-3222
Keywords
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PERIPLASMIC / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM NYSGXRC / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS
Function / homology
Protein of unknown function DUF4251 / Domain of unknown function (DUF4251) / Lipocalin - #410 / Lipocalin / Beta Barrel / Mainly Beta / Uncharacterized protein
Function and homology information
Biological species
Bacteroides vulgatus ATCC 8482 (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 8, 2008
Radiation
Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9793 Å / Relative weight: 1
Reflection
Resolution: 2.2→50 Å / Num. obs: 19563 / % possible obs: 99 % / Observed criterion σ(I): -5 / Redundancy: 3.9 % / Biso Wilson estimate: 59.608 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 9.8
Reflection shell
Resolution: 2.2→2.28 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.3 / % possible all: 98.9
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Processing
Software
Name
Version
Classification
SHELX
modelbuilding
REFMAC
5.3.0034
refinement
HKL-2000
datareduction
HKL-2000
datascaling
SHELX
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.805 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.293 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.27689
614
3.2 %
RANDOM
Rwork
0.24191
-
-
-
obs
0.24308
18689
98.87 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 65.509 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.5 Å2
0 Å2
0.48 Å2
2-
-
0.29 Å2
0 Å2
3-
-
-
1.28 Å2
Refinement step
Cycle: LAST / Resolution: 2.2→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2424
0
0
77
2501
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.022
2489
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.185
1.915
3381
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.876
5
323
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
41.525
25.954
131
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.321
15
405
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.811
15
10
X-RAY DIFFRACTION
r_chiral_restr
0.079
0.2
379
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
1936
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.139
0.3
1032
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.295
0.5
1660
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.139
0.5
200
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
0.111
0.3
46
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.159
0.5
14
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
2.901
2
1608
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
4.43
3
2517
X-RAY DIFFRACTION
r_scbond_it
5.856
4
1007
X-RAY DIFFRACTION
r_scangle_it
7.685
6
858
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
Refine LS restraints NCS
Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION
Ens-ID
Number
Type
Rms dev position (Å)
Weight position
2
947
tightpositional
0.58
0.1
1
155
mediumpositional
1.21
0.5
2
947
tightthermal
4.9
2.5
1
155
mediumthermal
4.49
5
LS refinement shell
Resolution: 2.2→2.257 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.396
43
-
Rwork
0.307
1372
-
obs
-
-
97.45 %
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