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Crystal structure of mouse isocitrate dehydrogenases 2 K256Q mutant complexed with isocitrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4L04
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 293 0.1 M ammonium formate, 24%(w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.11 41.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.15 α = 90 b = 58.15 β = 90 c = 206.915 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 270 2014-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.21 45.3 94.5 16 4.7 37204
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.21 2.34 71.7 3 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4L04 2.21 19.32 36284 1874 97 0.211 0.209 0.2114 0.243 0.2458 RANDOM 32.26
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.696 r_dihedral_angle_4_deg 15.775 r_dihedral_angle_3_deg 14.622 r_dihedral_angle_1_deg 5.977 r_long_range_B_refined 2.503 r_long_range_B_other 2.497 r_mcangle_it 1.128 r_mcangle_other 1.128 r_angle_refined_deg 1.08 r_scangle_other 0.942
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.696 r_dihedral_angle_4_deg 15.775 r_dihedral_angle_3_deg 14.622 r_dihedral_angle_1_deg 5.977 r_long_range_B_refined 2.503 r_long_range_B_other 2.497 r_mcangle_it 1.128 r_mcangle_other 1.128 r_angle_refined_deg 1.08 r_scangle_other 0.942 r_angle_other_deg 0.847 r_mcbond_it 0.641 r_mcbond_other 0.641 r_scbond_it 0.53 r_scbond_other 0.53 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 6507 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP model building