5LXE

F420-dependent glucose-6-phosphate dehydrogenase from Rhodococcus jostii RHA1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.15ammonium sulfate, sodium acetate pH 4.6, PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.1642.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.54α = 90
b = 88.12β = 90
c = 88.78γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2015-08-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.71, 2.25SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.4788.7898.70.050.99810.93.9106774
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)
11.471.50.55

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 REPLACEMENTTHROUGHOUT3B4Y1.4762.54101407529398.540.157780.156320.1853RANDOM25.021
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]
0.37-1.511.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.369
r_dihedral_angle_4_deg15.28
r_dihedral_angle_3_deg13.762
r_long_range_B_refined6.74
r_long_range_B_other6.74
r_dihedral_angle_1_deg6.577
r_scangle_other5.337
r_scbond_it3.52
r_scbond_other3.516
r_mcangle_other2.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.369
r_dihedral_angle_4_deg15.28
r_dihedral_angle_3_deg13.762
r_long_range_B_refined6.74
r_long_range_B_other6.74
r_dihedral_angle_1_deg6.577
r_scangle_other5.337
r_scbond_it3.52
r_scbond_other3.516
r_mcangle_other2.95
r_mcangle_it2.949
r_mcbond_it2.135
r_mcbond_other2.135
r_angle_refined_deg2.02
r_angle_other_deg1.074
r_chiral_restr0.129
r_bond_refined_d0.021
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms4882
Nucleic Acid Atoms
Solvent Atoms571
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing