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Crystal structure of S. aureus Homoserine Dehydrogenase at pH6.0
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 6 293 0.2M Magnesium acetate, 22% PEG8000, 0.1M Bis-Tris, pH6.0, 5% Glycerol, 1mM Serine
Crystal Properties Matthews coefficient Solvent content 2.43 49.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.46 α = 90 b = 116.32 β = 90 c = 118.35 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 2012-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.95372 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.2 118.35 98 0.071 16.8 8.2 50394 47.8
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 94.1 0.435 0.435 0.156 1.8 8 6957
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 39.5 47777 2556 97.7 0.202 0.2 0.2067 0.23 0.2355 RANDOM 34.59
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] -1.34 1.84 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.882 r_dihedral_angle_4_deg 16.949 r_dihedral_angle_3_deg 14.208 r_long_range_B_refined 6.607 r_long_range_B_other 6.606 r_dihedral_angle_1_deg 6.057 r_scangle_other 4.017 r_mcangle_it 3.541 r_mcangle_other 3.541 r_scbond_it 2.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.882 r_dihedral_angle_4_deg 16.949 r_dihedral_angle_3_deg 14.208 r_long_range_B_refined 6.607 r_long_range_B_other 6.606 r_dihedral_angle_1_deg 6.057 r_scangle_other 4.017 r_mcangle_it 3.541 r_mcangle_other 3.541 r_scbond_it 2.57 r_scbond_other 2.57 r_mcbond_it 2.224 r_mcbond_other 2.201 r_angle_refined_deg 1.371 r_angle_other_deg 0.938 r_chiral_restr 0.073 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 5770 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 115
Software Software Software Name Purpose REFMAC refinement HKL-3000 data collection SCALA data scaling PHASER phasing Coot model building PDB_EXTRACT data extraction MOSFLM data reduction