2B5W

Crystal structure of D38C glucose dehydrogenase mutant from Haloferax mediterranei


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2B5VPDB ENTRY 2B5V

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7290pH 7.00, temperature 290K, Vapor diffusion, hanging drop, VAPOR DIFFUSION, HANGING DROP, temperature 290 KK
Crystal Properties
Matthews coefficientSolvent content
3.261.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.534α = 90
b = 109.255β = 90
c = 151.893γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MIRRORS2002-01-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.2SRSPX14.2

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
11.62099.10.05825.855.166155
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)
11.61.6498.20.5432.69

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2B5V1.62062795335698.80.1540.186RANDOM21.16
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it16.687
r_scbond_it14.42
r_mcangle_it7.136
r_mcbond_it5.986
r_dihedral_angle_1_deg5.621
r_angle_refined_deg1.555
r_angle_other_deg0.854
r_symmetry_vdw_other0.298
r_symmetry_hbond_refined0.286
r_symmetry_vdw_refined0.276
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it16.687
r_scbond_it14.42
r_mcangle_it7.136
r_mcbond_it5.986
r_dihedral_angle_1_deg5.621
r_angle_refined_deg1.555
r_angle_other_deg0.854
r_symmetry_vdw_other0.298
r_symmetry_hbond_refined0.286
r_symmetry_vdw_refined0.276
r_nbd_other0.245
r_nbd_refined0.23
r_xyhbond_nbd_refined0.19
r_chiral_restr0.094
r_metal_ion_refined0.092
r_nbtor_other0.086
r_bond_refined_d0.023
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2767
Nucleic Acid Atoms
Solvent Atoms675
Heterogen Atoms67

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement