5H3E

Crystal structure of mouse isocitrate dehydrogenases 2 K256Q mutant complexed with isocitrate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4L04 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.42930.1 M ammonium formate, 24%(w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.1141.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.15α = 90
b = 58.15β = 90
c = 206.915γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2702014-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.0Photon FactoryAR-NE3A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.2145.394.5164.737204
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.212.3471.732.2

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 REPLACEMENTTHROUGHOUT4L042.2119.32362841874970.2110.2090.243RANDOM32.26
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]
0.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.696
r_dihedral_angle_4_deg15.775
r_dihedral_angle_3_deg14.622
r_dihedral_angle_1_deg5.977
r_long_range_B_refined2.503
r_long_range_B_other2.497
r_mcangle_it1.128
r_mcangle_other1.128
r_angle_refined_deg1.08
r_scangle_other0.942
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.696
r_dihedral_angle_4_deg15.775
r_dihedral_angle_3_deg14.622
r_dihedral_angle_1_deg5.977
r_long_range_B_refined2.503
r_long_range_B_other2.497
r_mcangle_it1.128
r_mcangle_other1.128
r_angle_refined_deg1.08
r_scangle_other0.942
r_angle_other_deg0.847
r_mcbond_it0.641
r_mcbond_other0.641
r_scbond_it0.53
r_scbond_other0.53
r_chiral_restr0.061
r_bond_refined_d0.007
r_gen_planes_refined0.003
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 Atoms6507
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPmodel building