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Crystal structure of S. aureus Homoserine Dehydrogenase at pH7.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DO5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.2M Magnesium acetate, 16% PEG3350, 0.1M HEPES, pH7.0, 5%Glycerol, 20% Iso-propanol
Crystal Properties Matthews coefficient Solvent content 2.45 49.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.64 α = 90 b = 116.88 β = 90 c = 118.62 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 225 mm CCD 2012-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97625 ESRF BM14
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 2.2 118.62 100 17.3 8.3 52050 47.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 100 0.442 0.442 0.162 1.7 8.4 7494
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 3DO5 2.2 34.7 49330 2651 100 0.205 0.203 0.2116 0.244 0.2489 RANDOM 34.58
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] -1.32 2.08 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.749 r_dihedral_angle_4_deg 16.906 r_dihedral_angle_3_deg 14.399 r_long_range_B_refined 6.462 r_long_range_B_other 6.462 r_dihedral_angle_1_deg 6.272 r_scangle_other 3.85 r_mcangle_other 3.588 r_mcangle_it 3.587 r_scbond_it 2.422
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.749 r_dihedral_angle_4_deg 16.906 r_dihedral_angle_3_deg 14.399 r_long_range_B_refined 6.462 r_long_range_B_other 6.462 r_dihedral_angle_1_deg 6.272 r_scangle_other 3.85 r_mcangle_other 3.588 r_mcangle_it 3.587 r_scbond_it 2.422 r_scbond_other 2.422 r_mcbond_it 2.249 r_mcbond_other 2.235 r_angle_refined_deg 1.338 r_angle_other_deg 0.964 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.003 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 5787 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 103
Software Software Software Name Purpose REFMAC refinement HKL-3000 data collection iMOSFLM data reduction SCALA data scaling PHASER phasing Coot model building PDB_EXTRACT data extraction MOSFLM data reduction