4MOW

Crystal structure of a putative glucose 1-dehydrogenase from Burkholderia cenocepacia J2315


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5289Morpheus G4: 37.5% MPD_P1K_P3350, 0.1M carboxylic acids, 0.1M buffer 1 pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.2946.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.99α = 90
b = 82.38β = 90
c = 168.35γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2013-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

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
11.955099.10.06620.356.32708307016517.7
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)
11.9521000.4394.036.385164

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 4JIG1.952066568354299.090.160690.158650.19848RANDOM26.232
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]
-0.46-0.541
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.574
r_dihedral_angle_4_deg12.963
r_dihedral_angle_3_deg11.285
r_dihedral_angle_1_deg5.835
r_long_range_B_refined5.47
r_long_range_B_other5.347
r_scangle_other3.214
r_mcangle_it2.244
r_mcangle_other2.243
r_scbond_it2.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.574
r_dihedral_angle_4_deg12.963
r_dihedral_angle_3_deg11.285
r_dihedral_angle_1_deg5.835
r_long_range_B_refined5.47
r_long_range_B_other5.347
r_scangle_other3.214
r_mcangle_it2.244
r_mcangle_other2.243
r_scbond_it2.07
r_scbond_other2.07
r_angle_refined_deg1.543
r_mcbond_it1.525
r_mcbond_other1.525
r_angle_other_deg0.835
r_chiral_restr0.096
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6820
Nucleic Acid Atoms
Solvent Atoms522
Heterogen Atoms8

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling