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Structural analysis of substrate-mimicking inhibitors in complex with Neisseria meningitidis 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase - the importance of accommodating the active site water
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HSN PDB ENTRY 4HSN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.3 pH 7.3
Crystal Properties Matthews coefficient Solvent content 2.57 52.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.439 α = 90 b = 133.733 β = 90 c = 147.237 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 110 CCD ADSC CCD 2013-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 Australian Synchrotron MX1
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 2.17 48.31 99.9 0.3 6.5 7.4 83610 1.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.17 2.21 98.7 1.2 7.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MIR THROUGHOUT PDB ENTRY 4HSN 2.17 98.99 79361 4166 99.9 0.20206 0.20075 0.2079 0.22673 0.233 RANDOM 24.895
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] -0.07 0.04 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.3 r_dihedral_angle_4_deg 18.12 r_dihedral_angle_3_deg 14.188 r_dihedral_angle_1_deg 5.08 r_angle_refined_deg 1.395 r_angle_other_deg 1.047 r_mcangle_it 0.93 r_scbond_it 0.924 r_mcbond_it 0.549 r_mcbond_other 0.549
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.3 r_dihedral_angle_4_deg 18.12 r_dihedral_angle_3_deg 14.188 r_dihedral_angle_1_deg 5.08 r_angle_refined_deg 1.395 r_angle_other_deg 1.047 r_mcangle_it 0.93 r_scbond_it 0.924 r_mcbond_it 0.549 r_mcbond_other 0.549 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 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_mcangle_other r_scbond_other r_scangle_it 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 10177 Nucleic Acid Atoms Solvent Atoms 633 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction