☰ Navigation Tabs
Structure of 3-isopropylmalate dehydrogenase in complex with the inhibitor and NAD+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HEX PDB ENTRY 1HEX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 293 4M sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH7.2
Crystal Properties Matthews coefficient Solvent content 3.91 68.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.507 α = 90 b = 103.507 β = 90 c = 186.418 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2008-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1 SPring-8 BL26B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.79 89.8 99.3 0.121 6.6 15425
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.79 2.9 99 0.495
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 PDB ENTRY 1HEX 2.79 25.88 14551 766 99.31 0.19988 0.19729 0.1995 0.24965 0.2472 RANDOM 33.649
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] -0.1 -0.05 -0.1 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.116 r_dihedral_angle_4_deg 22.989 r_dihedral_angle_3_deg 20.127 r_dihedral_angle_1_deg 6.039 r_scangle_it 3.946 r_scbond_it 2.232 r_angle_refined_deg 1.653 r_mcangle_it 1.321 r_mcbond_it 0.67 r_chiral_restr 0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.116 r_dihedral_angle_4_deg 22.989 r_dihedral_angle_3_deg 20.127 r_dihedral_angle_1_deg 6.039 r_scangle_it 3.946 r_scbond_it 2.232 r_angle_refined_deg 1.653 r_mcangle_it 1.321 r_mcbond_it 0.67 r_chiral_restr 0.099 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2595 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing