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Glutamate Racemase (MurI) from E. faecalis in complex with a 9-Benzyl Purine inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JFO PDB ENTRY 2JFO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 PROTEIN FORMULATED AT 10 MG/ML WITH 200MM AMMONIUM ACETATE PH 7.4, 5MM D-L GLUTAMATE, 1 MM TCEP AND CRYSTALLISED WITH 0.2 MM MGCL2 AND 20-25% PEG 3350, 100 MM TRIS PH 7.5, 20% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.402 α = 90 b = 69.432 β = 90 c = 165.12 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 ADSC CCD 2004-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.65 81.65 96.1 0.08 4.6 3.5 205055 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 1.65 1.69 99.9 0.13 5.1 3.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2JFO 1.65 81.65 56198 3003 94.8 0.152 0.15 0.184 0.2112 RANDOM 11.57
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] 0.66 -0.49 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.771 r_dihedral_angle_4_deg 14.686 r_dihedral_angle_3_deg 12.159 r_dihedral_angle_1_deg 5.386 r_scangle_it 3.694 r_scbond_it 2.426 r_mcangle_it 1.475 r_angle_refined_deg 1.461 r_mcbond_it 1.047 r_angle_other_deg 0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.771 r_dihedral_angle_4_deg 14.686 r_dihedral_angle_3_deg 12.159 r_dihedral_angle_1_deg 5.386 r_scangle_it 3.694 r_scbond_it 2.426 r_mcangle_it 1.475 r_angle_refined_deg 1.461 r_mcbond_it 1.047 r_angle_other_deg 0.92 r_symmetry_vdw_other 0.229 r_nbd_refined 0.227 r_nbd_other 0.196 r_symmetry_hbond_refined 0.195 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.175 r_symmetry_vdw_refined 0.118 r_chiral_restr 0.087 r_nbtor_other 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4049 Nucleic Acid Atoms Solvent Atoms 703 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing