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Homocitrate Synthase Lys4 bound to 2-OG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Homocitrate Synthase Lys4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 297 Na/KPO4, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 3.47 64.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.798 α = 90 b = 133.798 β = 90 c = 125.657 γ = 120
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 300 mm CCD 2007-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97872 APS 21-ID-G
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 2.72 40 96.4 0.056 12.3 3.8 33176 33176 -3
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 2.72 2.82 98.5 0.495 2.54 3.7 3362
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT Homocitrate Synthase Lys4 2.72 39.41 33176 33172 1681 96.2 0.18 0.18 0.177 0.1784 0.217 0.2182 RANDOM 66.186
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] -1.01 -0.5 -1.01 1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.137 r_dihedral_angle_3_deg 16.764 r_dihedral_angle_4_deg 16.261 r_dihedral_angle_1_deg 6.111 r_scangle_it 3.183 r_scbond_it 1.899 r_angle_refined_deg 1.453 r_mcangle_it 1.07 r_mcbond_it 0.535 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.137 r_dihedral_angle_3_deg 16.764 r_dihedral_angle_4_deg 16.261 r_dihedral_angle_1_deg 6.111 r_scangle_it 3.183 r_scbond_it 1.899 r_angle_refined_deg 1.453 r_mcangle_it 1.07 r_mcbond_it 0.535 r_nbtor_refined 0.309 r_nbd_refined 0.224 r_symmetry_hbond_refined 0.209 r_symmetry_vdw_refined 0.178 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.099 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5771 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 24
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling