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Structure of Helicobacter pylori type II dehydroquinase in complex with inhibitor compound (2R)-2-(4-methoxybenzyl)-3-dehydroquinic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C4V PDB ENTRY 2C4V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 20 MG/ML DEHYDROQUINASE; 12.5 MM 2R)-2-(4-METHOXYBENZYL)-3-DEHYDROQUINIC ACID, 50 MM TRIS-HCL PH 7.5, 1 MM 2-MERCAPTOETHANOL, 1 MM ETHYLENEDIAMINETETRAACETIC ACID, 200 MM SODIUM CHLORIDE; 31% (W/V) POLYETHYLENEGLYCOL 4000, 0.1 M SODIUM CITRATE PH 5.0
Crystal Properties Matthews coefficient Solvent content 2.4 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.56 α = 90 b = 100.56 β = 90 c = 105.449 γ = 90
Symmetry Space Group P 42 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 295 CCD ENRAF-NONIUS KAPPA CCD-2000 CONFOCAL MULTILAYER GRADED MIRRORS 2009-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591
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 2.75 35 99.9 0.04 22.68 3.6 14629 61.5
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 2.75 2.85 99.9 0.32 2.39 3.2
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2C4V 2.75 34.22 13844 748 99.75 0.1887 0.18508 0.1884 0.25033 0.2549 RANDOM 38.463
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] -0.72 -0.72 1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.532 r_dihedral_angle_3_deg 16.367 r_dihedral_angle_4_deg 11.513 r_dihedral_angle_1_deg 6.71 r_scangle_it 3.117 r_scbond_it 1.772 r_mcangle_it 1.667 r_angle_refined_deg 1.406 r_mcbond_it 0.892 r_angle_other_deg 0.889
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.532 r_dihedral_angle_3_deg 16.367 r_dihedral_angle_4_deg 11.513 r_dihedral_angle_1_deg 6.71 r_scangle_it 3.117 r_scbond_it 1.772 r_mcangle_it 1.667 r_angle_refined_deg 1.406 r_mcbond_it 0.892 r_angle_other_deg 0.889 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.18 r_symmetry_vdw_other 0.164 r_symmetry_hbond_refined 0.136 r_symmetry_vdw_refined 0.129 r_mcbond_other 0.098 r_nbtor_other 0.087 r_chiral_restr 0.077 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_nbd_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_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_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 3663 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing