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Homoserine dehydrogenase from Thermus thermophilus HB8 complexed with HSE and NADPH
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 4.2 70.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.619 α = 90 b = 119.619 β = 90 c = 144.338 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 315 2013-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
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 50 99.9 0.09 49 8.3 81149
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 2 2.07 100 0.343 6.6 8.2
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 5XDF 2 50 77030 4061 99.81 0.16099 0.159 0.1684 0.1997 0.2055 RANDOM 38.286
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] 0.04 0.02 0.04 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.696 r_dihedral_angle_4_deg 19.234 r_dihedral_angle_3_deg 14.405 r_long_range_B_refined 9.423 r_long_range_B_other 9.423 r_scangle_other 7.285 r_dihedral_angle_1_deg 7.054 r_mcangle_other 5.311 r_mcangle_it 5.307 r_scbond_it 5.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.696 r_dihedral_angle_4_deg 19.234 r_dihedral_angle_3_deg 14.405 r_long_range_B_refined 9.423 r_long_range_B_other 9.423 r_scangle_other 7.285 r_dihedral_angle_1_deg 7.054 r_mcangle_other 5.311 r_mcangle_it 5.307 r_scbond_it 5.165 r_scbond_other 5.163 r_mcbond_it 4.23 r_mcbond_other 4.23 r_angle_other_deg 3.875 r_angle_refined_deg 2.342 r_chiral_restr 0.16 r_bond_refined_d 0.026 r_gen_planes_other 0.023 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 4967 Nucleic Acid Atoms Solvent Atoms 536 Heterogen Atoms 173
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing