5H3F

Crystal structure of mouse isocitrate dehydrogenases 2 complexed with isocitrate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LWD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.62770.1 M sodium tribasic dehydrate, 11.5%(v/v) 2-propanol, 10.8%(w/v) PEG4000
Crystal Properties
Matthews coefficientSolvent content
6.1479.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.853α = 90
b = 135.853β = 90
c = 220.162γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2702014-06-15MSINGLE 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
13.2945.999.314.110.435964
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.293.49972.19.7

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 REPLACEMENTTHROUGHOUT1LWD3.2919.8933999178998.80.1940.1920.222RANDOM119.8
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]
0.40.20.4-1.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.694
r_dihedral_angle_3_deg15.226
r_dihedral_angle_4_deg12.628
r_long_range_B_refined8.181
r_long_range_B_other8.181
r_dihedral_angle_1_deg5.556
r_scangle_other5.496
r_mcangle_other4.973
r_mcangle_it4.972
r_scbond_other3.112
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.694
r_dihedral_angle_3_deg15.226
r_dihedral_angle_4_deg12.628
r_long_range_B_refined8.181
r_long_range_B_other8.181
r_dihedral_angle_1_deg5.556
r_scangle_other5.496
r_mcangle_other4.973
r_mcangle_it4.972
r_scbond_other3.112
r_scbond_it3.111
r_mcbond_it2.974
r_mcbond_other2.969
r_angle_refined_deg1.029
r_angle_other_deg0.839
r_chiral_restr0.06
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 Atoms6604
Nucleic Acid Atoms
Solvent Atoms4
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPmodel building