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Crystal structure of glutamate racemase from Listeria monocytogenes in complex with succinic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HFR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 PEG3350 15%, Succinic acid 0.1M, pH 7, 10mm L-Glutamic acid, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.39 48.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.42 α = 90 b = 66.42 β = 90 c = 258.774 γ = 90
Symmetry Space Group P 43 21 2
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 315r mirrors 2009-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97934 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.65 50 97.9 0.073 0.073 39.4 6.5 69724 69724 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 92.6 0.671 0.671 2.4 4.9
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 (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 3hfr 1.65 50 66078 66078 3512 98.01 0.17307 0.1711 0.1971 0.21145 0.2346 RANDOM 11.555
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] 0.98 0.98 -1.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.906 r_dihedral_angle_4_deg 14.149 r_dihedral_angle_3_deg 12.635 r_dihedral_angle_1_deg 5.664 r_scangle_it 4.759 r_scbond_it 3.11 r_mcangle_it 1.687 r_angle_refined_deg 1.677 r_angle_other_deg 0.998 r_mcbond_it 0.971
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.906 r_dihedral_angle_4_deg 14.149 r_dihedral_angle_3_deg 12.635 r_dihedral_angle_1_deg 5.664 r_scangle_it 4.759 r_scbond_it 3.11 r_mcangle_it 1.687 r_angle_refined_deg 1.677 r_angle_other_deg 0.998 r_mcbond_it 0.971 r_mcbond_other 0.31 r_chiral_restr 0.108 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4071 Nucleic Acid Atoms Solvent Atoms 483 Heterogen Atoms 18
Software Software Software Name Purpose HKL-2000 data collection HKL-3000 phasing REFMAC refinement Coot model building HKL-3000 data reduction HKL-3000 data scaling