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Helicobacter pylori glutamate racemase in complex with D-glutamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JFY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1 M Tris pH 8.5, 0.1 M Magnesium sulfate and 20 % (w/v) PEG4000
Crystal Properties Matthews coefficient Solvent content 2.43 49.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.087 α = 90 b = 72.95 β = 113.594 c = 70.159 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2025-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.060 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.43 64.294 87.4 0.998 9.1 7.1 64959
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.43 1.59 0.558
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.432 64.294 64959 3293 64.792 0.156 0.1543 0.1543 0.1958 0.1958 25.247
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] 0.121 0.05 -0.065 -0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.5 r_dihedral_angle_3_deg 14.138 r_lrange_it 9.536 r_lrange_other 9.536 r_dihedral_angle_2_deg 8.711 r_scangle_it 7.824 r_scangle_other 7.823 r_dihedral_angle_1_deg 6.721 r_scbond_other 5.195 r_scbond_it 5.194
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.5 r_dihedral_angle_3_deg 14.138 r_lrange_it 9.536 r_lrange_other 9.536 r_dihedral_angle_2_deg 8.711 r_scangle_it 7.824 r_scangle_other 7.823 r_dihedral_angle_1_deg 6.721 r_scbond_other 5.195 r_scbond_it 5.194 r_mcangle_it 4.393 r_mcangle_other 4.392 r_mcbond_it 3.022 r_mcbond_other 3.022 r_angle_refined_deg 2.185 r_angle_other_deg 0.725 r_symmetry_nbd_refined 0.331 r_nbd_other 0.266 r_symmetry_xyhbond_nbd_refined 0.236 r_nbd_refined 0.231 r_symmetry_nbd_other 0.202 r_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.185 r_chiral_restr 0.114 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4024 Nucleic Acid Atoms Solvent Atoms 364 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing