2WVZ | pdb_00002wvz

Structure of the Family GH92 Inverting Mannosidase BT3990 from Bacteroides thetaiotaomicron VPI-5482


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WVXPDB ENTRY 2WVX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
120% V/V 3350, 100MM MIBS BUFFER (PH 6.0)
Crystal Properties
Matthews coefficientSolvent content
2.958

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.9α = 90
b = 150.19β = 90
c = 382.29γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2008-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.46088.40.136.23.5156201239.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.5389.30.492.13.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2WVX2.4191.14130782685988.120.203940.201120.20.257180.26RANDOM32.364
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]
2.261.04-3.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.705
r_dihedral_angle_4_deg18.027
r_dihedral_angle_3_deg16.317
r_dihedral_angle_1_deg6.367
r_scangle_it2.376
r_scbond_it1.496
r_angle_refined_deg1.321
r_mcangle_it0.945
r_mcbond_it0.505
r_chiral_restr0.085
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms23935
Nucleic Acid Atoms
Solvent Atoms792
Heterogen Atoms98

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing