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Crystal structure of chorismate mutase from Helicobacter pylori in complex with prephenate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YBZ 1YBZ, 2D8D and 3RMI experimental model PDB 2D8D 1YBZ, 2D8D and 3RMI experimental model PDB 3RMI 1YBZ, 2D8D and 3RMI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 0.1 M MES pH 6.5, 0.2 M ammonium acetate, 35% glycerol ethoxylate, 0.5 mM chorismate acid
Crystal Properties Matthews coefficient Solvent content 2.27 45.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.869 α = 90 b = 63.526 β = 90 c = 166.918 γ = 90
Symmetry Space Group C 2 2 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 QUANTUM 315r 2015-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953700 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 41.73 99.1 0.121 0.996 11.6 8.9 10877
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.21 2.28 99.8 0.372 0.911 4.1 8.6
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 1YBZ, 2D8D and 3RMI 2.3 19.43 9097 464 99.73 0.2076 0.20611 0.23691 0.2502 RANDOM 38.789
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] -0.23 0.55 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.246 r_dihedral_angle_4_deg 26.401 r_dihedral_angle_3_deg 19.034 r_long_range_B_refined 7.394 r_long_range_B_other 7.392 r_dihedral_angle_1_deg 6.368 r_scangle_other 5.569 r_mcangle_it 3.894 r_mcangle_other 3.892 r_scbond_it 3.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.246 r_dihedral_angle_4_deg 26.401 r_dihedral_angle_3_deg 19.034 r_long_range_B_refined 7.394 r_long_range_B_other 7.392 r_dihedral_angle_1_deg 6.368 r_scangle_other 5.569 r_mcangle_it 3.894 r_mcangle_other 3.892 r_scbond_it 3.412 r_angle_other_deg 3.41 r_scbond_other 3.41 r_mcbond_other 2.523 r_mcbond_it 2.522 r_angle_refined_deg 1.301 r_chiral_restr 0.329 r_bond_refined_d 0.01 r_gen_planes_other 0.006 r_gen_planes_refined 0.005 r_bond_other_d 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 1488 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing