8HP3 | pdb_00008hp3

Crystal structure of meso-diaminopimelate dehydrogenase from Prevotella timonensis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2980.1 M HEPES, pH 7.5, 0.1 M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.5151.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.73α = 90
b = 189.6β = 90
c = 101.82γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELBruker PHOTON II2021-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEBRUKER D8 QUEST1.54178

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
13.0747.5399.80.1737.84.718754
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)
13.073.280.66

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3.0747.531786687099.630.20070.197860.20.260510.26RANDOM52.028
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]
-2.660.042.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.821
r_dihedral_angle_4_deg20.002
r_dihedral_angle_3_deg18.302
r_long_range_B_refined9.711
r_long_range_B_other9.71
r_dihedral_angle_1_deg7.827
r_scangle_other6.677
r_mcangle_it6.134
r_mcangle_other6.133
r_scbond_it4.157
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6804
Nucleic Acid Atoms
Solvent Atoms30
Heterogen Atoms220

Software

Software
Software NamePurpose
Aimlessdata scaling
HKL-2000data reduction