3D33

Crystal structure of a duf3244 family protein with an immunoglobulin-like beta-sandwich fold (bvu_0276) from bacteroides vulgatus atcc 8482 at 1.70 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.92770.2000M MgFormate, 20.0000% PEG-3350, No Buffer pH 5.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthew coefficientSolvent content
2.4249.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.562α = 90
b = 55.179β = 94.31
c = 47.116γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat mirror (vertical focusing)2008-04-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-1SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.728.67799.60.0980.0984.67.42511624.306
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7495.70.8710.8710.971763

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.728.67725099128399.630.1760.1740.22RANDOM18.342
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.37-0.050.32-0.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.188
r_dihedral_angle_4_deg16.805
r_dihedral_angle_3_deg12.758
r_dihedral_angle_1_deg6.224
r_scangle_it5.982
r_scbond_it4.374
r_mcangle_it2.717
r_mcbond_it1.914
r_angle_refined_deg1.494
r_angle_other_deg0.845
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.188
r_dihedral_angle_4_deg16.805
r_dihedral_angle_3_deg12.758
r_dihedral_angle_1_deg6.224
r_scangle_it5.982
r_scbond_it4.374
r_mcangle_it2.717
r_mcbond_it1.914
r_angle_refined_deg1.494
r_angle_other_deg0.845
r_mcbond_other0.552
r_nbd_other0.21
r_nbd_refined0.193
r_symmetry_vdw_other0.18
r_nbtor_refined0.175
r_symmetry_hbond_refined0.171
r_symmetry_vdw_refined0.134
r_xyhbond_nbd_refined0.116
r_nbtor_other0.089
r_chiral_restr0.087
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_gen_planes_other0.001
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1439
Nucleic Acid Atoms
Solvent Atoms283
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SOLVEphasing
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction