2W90

Geobacillus stearothermophilus 6-phosphogluconate dehydrogenase with bound 6- phosphogluconate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.40.2 M LISO4, 2.2 M (NH4)2SO4, pH 7.4
Crystal Properties
Matthews coefficientSolvent content
2.7655.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.95α = 90
b = 119.5β = 90
c = 142.24γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTORODIAL FOCUSING MIRROR2007-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.25099.40.1210.436.2857708
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)
12.22.2599.60.593.636.22

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 2ZI02.271.0755339294799.30.1740.1710.234RANDOM32.58
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]
1.74-2.81.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.937
r_dihedral_angle_4_deg17.411
r_dihedral_angle_3_deg16.318
r_dihedral_angle_1_deg5.43
r_scangle_it2.733
r_scbond_it2.043
r_angle_refined_deg1.278
r_mcangle_it1.164
r_angle_other_deg0.916
r_mcbond_it0.912
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.937
r_dihedral_angle_4_deg17.411
r_dihedral_angle_3_deg16.318
r_dihedral_angle_1_deg5.43
r_scangle_it2.733
r_scbond_it2.043
r_angle_refined_deg1.278
r_mcangle_it1.164
r_angle_other_deg0.916
r_mcbond_it0.912
r_symmetry_vdw_other0.238
r_symmetry_vdw_refined0.215
r_nbd_refined0.201
r_nbd_other0.185
r_xyhbond_nbd_refined0.184
r_nbtor_refined0.181
r_mcbond_other0.177
r_symmetry_hbond_refined0.175
r_nbtor_other0.087
r_chiral_restr0.076
r_xyhbond_nbd_other0.028
r_bond_refined_d0.012
r_bond_other_d0.005
r_gen_planes_refined0.005
r_symmetry_hbond_other0.003
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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 Atoms7344
Nucleic Acid Atoms
Solvent Atoms754
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing