2VWH

Haloferax mediterranei glucose dehydrogenase in complex with NADP, Zn and glucose.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.51.5M SODIUM CITRATE, 0.1M SODIUM HEPES PH8.0, 10MM NADP, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
3.363

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.492α = 90
b = 112.703β = 90
c = 151.452γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray290IMAGE PLATEMARRESEARCHMIRRORS2001-01-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
12.033098.90.0818.36.834033
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)
12.032.0889.90.283.72.3

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 2B5V2.0314.87322421718990.1350.1340.159RANDOM29.38
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]
0.01-0.040.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.103
r_dihedral_angle_4_deg14.371
r_dihedral_angle_3_deg11.605
r_scangle_it10.403
r_scbond_it7.774
r_mcbond_it7.405
r_mcangle_it7.19
r_dihedral_angle_1_deg5.287
r_angle_refined_deg1.224
r_angle_other_deg0.872
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.103
r_dihedral_angle_4_deg14.371
r_dihedral_angle_3_deg11.605
r_scangle_it10.403
r_scbond_it7.774
r_mcbond_it7.405
r_mcangle_it7.19
r_dihedral_angle_1_deg5.287
r_angle_refined_deg1.224
r_angle_other_deg0.872
r_symmetry_vdw_other0.206
r_nbd_refined0.198
r_nbd_other0.19
r_nbtor_refined0.173
r_xyhbond_nbd_refined0.156
r_symmetry_vdw_refined0.15
r_nbtor_other0.084
r_symmetry_hbond_refined0.076
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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 Atoms2770
Nucleic Acid Atoms
Solvent Atoms148
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing