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H.pylori type II dehydroquinase in complex with FA1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C4W PDB ENTRY 2C4W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.8 10MG/ML PROTEIN AGAINST 30% 1,4 BUTANDIOL, 0.1M SODIUM ACETATE PH 4.5 USING SITTING DROP METHOD
Crystal Properties Matthews coefficient Solvent content 3.37 63.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.863 α = 90 b = 103.863 β = 90 c = 217.531 γ = 120
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 MARRESEARCH MIRRORS 2002-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.5 SRS PX9.5
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 3.08 46.6 90.4 0.09 10 4.5 43781 78
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 3.1 3.15 81.6 0.85 1.2 3
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 2C4W 3.1 25 35869 3968 83.8 0.21 0.207 0.1944 0.237 0.2252 RANDOM 61.18
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] 1.05 0.52 1.05 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.766 r_dihedral_angle_3_deg 20.972 r_dihedral_angle_4_deg 8.844 r_dihedral_angle_1_deg 7.733 r_angle_refined_deg 2.076 r_scangle_it 0.786 r_scbond_it 0.611 r_symmetry_hbond_refined 0.529 r_mcangle_it 0.421 r_nbtor_refined 0.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.766 r_dihedral_angle_3_deg 20.972 r_dihedral_angle_4_deg 8.844 r_dihedral_angle_1_deg 7.733 r_angle_refined_deg 2.076 r_scangle_it 0.786 r_scbond_it 0.611 r_symmetry_hbond_refined 0.529 r_mcangle_it 0.421 r_nbtor_refined 0.338 r_mcbond_it 0.317 r_nbd_refined 0.264 r_symmetry_vdw_refined 0.234 r_xyhbond_nbd_refined 0.183 r_chiral_restr 0.125 r_bond_refined_d 0.024 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 14224 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing