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Homoserine dehydrogenase from Thermus thermophilus HB8 unliganded form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XDF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 Sodium formate, CAPS pH 10.0
Crystal Properties Matthews coefficient Solvent content 4.17 70.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.197 α = 90 b = 119.197 β = 90 c = 144.547 γ = 120
Symmetry Space Group P 32 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 ADSC QUANTUM 210 2014-06-22 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 1.83 50 100 0.114 48.7 8.4 104929
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) 1 1.83 1.86 100 0.359 7 8.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5XDF 1.83 20 99528 5231 99.84 0.14971 0.14825 0.17707 0.1894 RANDOM 28.115
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] 0.23 0.12 0.23 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.322 r_dihedral_angle_4_deg 20.02 r_dihedral_angle_3_deg 12.948 r_long_range_B_refined 9.222 r_long_range_B_other 9.221 r_dihedral_angle_1_deg 7.53 r_scangle_other 6.847 r_scbond_it 4.697 r_scbond_other 4.697 r_mcangle_it 4.365
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.322 r_dihedral_angle_4_deg 20.02 r_dihedral_angle_3_deg 12.948 r_long_range_B_refined 9.222 r_long_range_B_other 9.221 r_dihedral_angle_1_deg 7.53 r_scangle_other 6.847 r_scbond_it 4.697 r_scbond_other 4.697 r_mcangle_it 4.365 r_mcangle_other 4.365 r_angle_other_deg 3.724 r_mcbond_it 3.395 r_mcbond_other 3.394 r_angle_refined_deg 2.514 r_chiral_restr 0.174 r_bond_refined_d 0.029 r_gen_planes_other 0.026 r_gen_planes_refined 0.014 r_bond_other_d 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 4984 Nucleic Acid Atoms Solvent Atoms 759 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing