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Crystal structure of homoisocitrate dehydrogenase in complex with a designed inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X0L PDB ENTRY 1X0L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.9 293 40% MPD, 0.1M CITRATE(PH 4.85), 2MM NAD+, 1MM MGSO4, 1MM THIA-HOMOCITARATE , VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 3.17 61.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 220.967 α = 90 b = 93.695 β = 97.68 c = 88.802 γ = 90
Symmetry Space Group C 1 2 1
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 RIGAKU JUPITER 210 2008-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0 SPring-8 BL26B1
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 2.6 109.8 99.8 55158 55158
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1X0L 2.6 44.02 52340 52340 2799 99.8 0.172 0.172 0.169 0.1743 0.231 0.237 RANDOM 33.46
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 0.03 0.04 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.422 r_dihedral_angle_4_deg 20.262 r_dihedral_angle_3_deg 19.375 r_dihedral_angle_1_deg 6.315 r_scangle_it 3.721 r_scbond_it 2.16 r_angle_refined_deg 1.574 r_mcangle_it 1.283 r_mcbond_it 0.663 r_chiral_restr 0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.422 r_dihedral_angle_4_deg 20.262 r_dihedral_angle_3_deg 19.375 r_dihedral_angle_1_deg 6.315 r_scangle_it 3.721 r_scbond_it 2.16 r_angle_refined_deg 1.574 r_mcangle_it 1.283 r_mcbond_it 0.663 r_chiral_restr 0.099 r_bond_refined_d 0.014 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 10076 Nucleic Acid Atoms Solvent Atoms 388 Heterogen Atoms 185
Software Software Software Name Purpose BSS data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling