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Crystal structure of homoisocitrate dehydrogenase from Thermus thermophilus in complex with homoisocitrate, magnesium ion (II) and NADH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X0L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.1 M Tris-HCl (pH 8.5), 1.5 M Ammonium sulfate, 12 % (v/v) Glycerol
Crystal Properties Matthews coefficient Solvent content 3.29 62.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 159.663 α = 90 b = 159.663 β = 90 c = 148.517 γ = 90
Symmetry Space Group P 43 21 2
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 210 2014-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 2.5 50 95.1 0.111 18.7 3.9 66916 3.9 3.9
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 1X0L 2.5 50 60576 2997 95.09 0.15255 0.14995 0.1595 0.20495 0.2093 RANDOM 32.805
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.272 r_dihedral_angle_4_deg 20.133 r_dihedral_angle_3_deg 17.534 r_long_range_B_refined 6.512 r_long_range_B_other 6.512 r_dihedral_angle_1_deg 5.774 r_scangle_other 4.004 r_scbond_it 2.493 r_scbond_other 2.493 r_mcangle_other 2.461
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.272 r_dihedral_angle_4_deg 20.133 r_dihedral_angle_3_deg 17.534 r_long_range_B_refined 6.512 r_long_range_B_other 6.512 r_dihedral_angle_1_deg 5.774 r_scangle_other 4.004 r_scbond_it 2.493 r_scbond_other 2.493 r_mcangle_other 2.461 r_mcangle_it 2.46 r_mcbond_it 1.537 r_mcbond_other 1.534 r_angle_refined_deg 1.457 r_angle_other_deg 0.9 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 10076 Nucleic Acid Atoms Solvent Atoms 563 Heterogen Atoms 530
Software Software Software Name Purpose REFMAC refinement Coot refinement HKL-2000 data scaling PHASER phasing