2WVY

STRUCTURE OF THE FAMILY GH92 INVERTING MANNOSIDASE BT2199 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
110% V/V 2-METHYL-2, 4-PENTANEDIOL, 1.2 M C3H2O4NA2 AND 0.1M 1, 3-BIS(TRIS(HYDROXYMETHYL)METHYLAMINO)PROPANETE (PH 7.5)
Crystal Properties
Matthews coefficientSolvent content
2.8457

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 154.934α = 90
b = 163.765β = 90
c = 115.533γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2008-11-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
12.25601000.13148.2139549228.9
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)
12.252.371000.548.3

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2WVX2.26115.47129149682398.350.170640.168760.20656RANDOM16.105
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]
1.28-0.88-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.582
r_dihedral_angle_4_deg14.595
r_dihedral_angle_3_deg14.285
r_dihedral_angle_1_deg9.402
r_scangle_it2.552
r_scbond_it1.546
r_angle_refined_deg1.207
r_mcangle_it0.911
r_mcbond_it0.463
r_chiral_restr0.085
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.582
r_dihedral_angle_4_deg14.595
r_dihedral_angle_3_deg14.285
r_dihedral_angle_1_deg9.402
r_scangle_it2.552
r_scbond_it1.546
r_angle_refined_deg1.207
r_mcangle_it0.911
r_mcbond_it0.463
r_chiral_restr0.085
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms17346
Nucleic Acid Atoms
Solvent Atoms1080
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing