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Crystal Structure of Helicobacter pylori beta clamp in complex with 3, 4-Difluorobenzamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RKI PDB ENTRY 4RKI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 20% V/V PEG MME550, 6% W/V PEG 20000, 0.01M MGCL2, 0.1M MOPS/HEPES-NA PH 7.3, 0.2M AMMONIUM CITRATE
Crystal Properties Matthews coefficient Solvent content 2.66 53.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.071 α = 90 b = 66.383 β = 115.43 c = 82.778 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 287 CCD MARRESEARCH 2015-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 2.07 50 98.5 0.06 33.17 6.8 26589 0.3
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 2.07 50 90.9 0.42 3 5.8
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 4RKI 2.07 74.76 25206 1342 98.53 0.21446 0.2127 0.2159 0.24732 0.2535 RANDOM 49.506
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] 3.28 2.23 -3.52 -1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.599 r_dihedral_angle_4_deg 15.393 r_dihedral_angle_3_deg 15.093 r_dihedral_angle_1_deg 6.761 r_long_range_B_refined 4.19 r_long_range_B_other 4.141 r_mcangle_it 2.461 r_mcangle_other 2.461 r_scangle_other 2.34 r_mcbond_it 1.427
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.599 r_dihedral_angle_4_deg 15.393 r_dihedral_angle_3_deg 15.093 r_dihedral_angle_1_deg 6.761 r_long_range_B_refined 4.19 r_long_range_B_other 4.141 r_mcangle_it 2.461 r_mcangle_other 2.461 r_scangle_other 2.34 r_mcbond_it 1.427 r_mcbond_other 1.427 r_scbond_it 1.355 r_scbond_other 1.355 r_angle_refined_deg 1.276 r_angle_other_deg 0.848 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2870 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement CCP4 phasing