3K11

Crystal structure of Putative glycosyl hydrolase (NP_813087.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.80 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62775.0000% PEG-6000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.8167.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.135α = 90
b = 121.135β = 90
c = 182.812γ = 120
Symmetry
Space GroupP 63 2 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 BL9-20.91162,0.97936,0.97919SSRLBL9-2

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
11.829.9881000.1010.10114.37.37372522.138
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)
11.81.851000.7640.76417.35333

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 DIFFRACTIONMADTHROUGHOUT1.829.98873676371499.960.1510.150.171RANDOM29.571
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]
1.610.811.61-2.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.443
r_dihedral_angle_4_deg22.615
r_dihedral_angle_3_deg12.368
r_scangle_it6.089
r_dihedral_angle_1_deg5.038
r_scbond_it4.819
r_mcangle_it2.535
r_mcbond_it1.988
r_angle_refined_deg1.544
r_angle_other_deg1.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.443
r_dihedral_angle_4_deg22.615
r_dihedral_angle_3_deg12.368
r_scangle_it6.089
r_dihedral_angle_1_deg5.038
r_scbond_it4.819
r_mcangle_it2.535
r_mcbond_it1.988
r_angle_refined_deg1.544
r_angle_other_deg1.08
r_mcbond_other0.549
r_symmetry_vdw_refined0.241
r_symmetry_vdw_other0.239
r_nbd_refined0.225
r_symmetry_hbond_refined0.193
r_nbtor_refined0.191
r_nbd_other0.185
r_xyhbond_nbd_refined0.178
r_chiral_restr0.101
r_nbtor_other0.089
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3489
Nucleic Acid Atoms
Solvent Atoms468
Heterogen Atoms88

Software

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