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Crystal structure of homoserine dehydrogenase from Thermoplasma volcanium
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 0.2 M Lithium sulfate, 0.12 M Tris buffer, 2 M Ammonium sulfate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.76 55.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.404 α = 90 b = 108.404 β = 90 c = 60.458 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 2008-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID
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 1.9 37.2 100 0.102 8 11 32528 32528 33.2
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 1.9 1.97 100 0.763 3.47 10.9 3209
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.9 37.2 32410 32410 1640 99.75 0.157 0.157 0.156 0.1553 0.177 0.1768 RANDOM 22.27
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] -0.22 -0.11 -0.22 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.793 r_dihedral_angle_4_deg 19.536 r_dihedral_angle_3_deg 15.589 r_dihedral_angle_1_deg 5.973 r_scangle_it 3.884 r_scbond_it 2.6 r_mcangle_it 1.58 r_angle_refined_deg 1.507 r_mcbond_it 0.997 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.793 r_dihedral_angle_4_deg 19.536 r_dihedral_angle_3_deg 15.589 r_dihedral_angle_1_deg 5.973 r_scangle_it 3.884 r_scbond_it 2.6 r_mcangle_it 1.58 r_angle_refined_deg 1.507 r_mcbond_it 0.997 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.224 r_nbd_refined 0.209 r_symmetry_hbond_refined 0.193 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.112 r_bond_refined_d 0.016 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2550 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms 20
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction SHELXD phasing MLPHARE phasing DM phasing SOLVE phasing RESOLVE phasing HKL-3000 phasing