3JYS

Crystal structure of SusD superfamily protein (YP_001298690.1) from Bacteroides vulgatus ATCC 8482 at 2.00 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.82770.2000M MgCl2, 20.0000% PEG-3350, No Buffer pH 5.8, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.448.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.929α = 90
b = 63.929β = 90
c = 266.398γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat collimating mirror, toroid focusing mirror2009-05-15MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.91162,0.97936SSRLBL9-2

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
1229.1111000.0750.07516.87.13869032.57
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)
122.051000.6430.6431.27.32786

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 DIFFRACTIONMADTHROUGHOUT229.11138586193199.930.1790.1780.198RANDOM32.083
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]
1.331.33-2.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.632
r_dihedral_angle_3_deg14.618
r_dihedral_angle_4_deg8.307
r_dihedral_angle_1_deg6.145
r_scangle_it3.059
r_scbond_it2.046
r_angle_refined_deg1.476
r_mcangle_it1.25
r_angle_other_deg0.967
r_mcbond_it0.724
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.632
r_dihedral_angle_3_deg14.618
r_dihedral_angle_4_deg8.307
r_dihedral_angle_1_deg6.145
r_scangle_it3.059
r_scbond_it2.046
r_angle_refined_deg1.476
r_mcangle_it1.25
r_angle_other_deg0.967
r_mcbond_it0.724
r_mcbond_other0.198
r_chiral_restr0.093
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3814
Nucleic Acid Atoms
Solvent Atoms266
Heterogen Atoms1

Software

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