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Type II Dehydroquinase from H. pylori in complex with AH9095
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DHQ PDB ENTRY 2DHQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.2 10MG/ML PROTEIN CRYSTLLISED AGAINST 1.0M NA ACETATE, 0.1M IMIDAZOLE-HCL PH 8.2
Crystal Properties Matthews coefficient Solvent content 2.13 37.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.37 α = 90 b = 131.37 β = 90 c = 131.37 γ = 90
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 MIRRORS 2001-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 SRS PX9.6
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 1.55 50 100 0.04 24 12.2 27302 20.2
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 1.55 1.58 99.9 0.74 2 5.5
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 2DHQ 1.55 25 23103 2564 94.1 0.156 0.152 0.1663 0.19 0.2 RANDOM 24.93
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 35.598 r_dihedral_angle_3_deg 14.378 r_dihedral_angle_4_deg 10.861 r_dihedral_angle_1_deg 7.458 r_scangle_it 3.27 r_scbond_it 2.379 r_mcangle_it 2.1 r_mcbond_it 1.878 r_angle_refined_deg 1.532 r_angle_other_deg 0.885
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.598 r_dihedral_angle_3_deg 14.378 r_dihedral_angle_4_deg 10.861 r_dihedral_angle_1_deg 7.458 r_scangle_it 3.27 r_scbond_it 2.379 r_mcangle_it 2.1 r_mcbond_it 1.878 r_angle_refined_deg 1.532 r_angle_other_deg 0.885 r_symmetry_hbond_refined 0.301 r_xyhbond_nbd_refined 0.24 r_nbd_refined 0.235 r_symmetry_vdw_other 0.223 r_symmetry_vdw_refined 0.21 r_nbtor_refined 0.178 r_nbd_other 0.172 r_chiral_restr 0.086 r_nbtor_other 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 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_mcbond_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 1275 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling EPMR phasing