7AOB

Crystal structure of Thermaerobacter marianensis malate dehydrogenase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION729320% PEG 20K, 100 mM pH 7,0, 5% glycerol
Crystal Properties
Matthews coefficientSolvent content
3.0659.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.91α = 90
b = 150.48β = 90
c = 153.97γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-10-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.979968ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.1248.94930.9911.8386293
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.122.2593.80.8873.88

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 REPLACEMENTTHROUGHOUT3NEP2.1248.9482841345293.20.1640.1620.205RANDOM26.92
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]
-0.281.27-0.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.759
r_dihedral_angle_4_deg18.713
r_dihedral_angle_3_deg14.013
r_dihedral_angle_1_deg6.53
r_angle_refined_deg1.483
r_angle_other_deg1.313
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.759
r_dihedral_angle_4_deg18.713
r_dihedral_angle_3_deg14.013
r_dihedral_angle_1_deg6.53
r_angle_refined_deg1.483
r_angle_other_deg1.313
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.008
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9300
Nucleic Acid Atoms
Solvent Atoms849
Heterogen Atoms95

Software

Software
Software NamePurpose
REFMACrefinement
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling