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STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE IN COMPLEX WITH INHIBITOR COMPOUND (4R,6R,7S)-2-(2-Cyclopropyl)ethyl-4,6,7- trihydroxy-4,5,6,7-tetrahydrobenzo(b)thiophene-4-carboxylic 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 6.2 50 MM TRIS-HCL PH 7.5 1 MM 2-MERCAPTOETHANOL 1 MM ETHYLENEDIAMINETETRAACETIC ACID 200 MM SODIUM CHLORIDE 12.5 MM (4R, 6R, 7S)- 2-(2-CYCLOPROPYL)ETHYL-4,6,7-TRIHYDROXY-4,5,6, 7-TETRAHYDROBENZO[B]THIOPHENE-4-CARBOXYLIC ACID 32% (W/V) POLYETHYLENEGLYCOL 4000 100 M SODIUM CITRATE PH 6.2
Crystal Properties Matthews coefficient Solvent content 2.2 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.64 α = 90 b = 99.64 β = 90 c = 99.64 γ = 90
Symmetry Space Group P 42 3 2
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 2009-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 1.85 40 99.8 0.1 4.9 38.9 14986 19.7
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 1.85 1.95 100 0.32 2.4 39.9
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 1.85 15 14163 770 99.83 0.18187 0.18032 0.1853 0.20981 0.2136 RANDOM 19.598
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.759 r_dihedral_angle_3_deg 14.994 r_dihedral_angle_4_deg 6.368 r_dihedral_angle_1_deg 5.784 r_scangle_it 3.608 r_scbond_it 2.239 r_mcangle_it 1.934 r_angle_refined_deg 1.374 r_mcbond_it 1.087 r_angle_other_deg 0.886
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.759 r_dihedral_angle_3_deg 14.994 r_dihedral_angle_4_deg 6.368 r_dihedral_angle_1_deg 5.784 r_scangle_it 3.608 r_scbond_it 2.239 r_mcangle_it 1.934 r_angle_refined_deg 1.374 r_mcbond_it 1.087 r_angle_other_deg 0.886 r_mcbond_other 0.243 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.184 r_symmetry_hbond_refined 0.182 r_nbd_other 0.178 r_nbtor_refined 0.174 r_symmetry_vdw_other 0.169 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.085 r_nbtor_other 0.085 r_bond_refined_d 0.015 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_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 1153 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing