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Crystal Structure of Helicobacter pylori beta clamp bound to DNA ligase peptide
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 6% W/V PEG 20,000, 20% V/V PEG MME550, 0.01M MGCL2, 0.1M MOPS/HEPES-NA PH7.3, 0.2M AMMONIUM CITRATE
Crystal Properties Matthews coefficient Solvent content 2.52 51.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.829 α = 90 b = 146.147 β = 90 c = 179.075 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 289 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 2.9 50 94.3 0.1 11 4.2 35997 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 2.9 50 95 0.52 1.9 4
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 2.9 113.23 34649 1847 94.26 0.23302 0.23147 0.2362 0.26154 0.2654 RANDOM
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 35.645 r_dihedral_angle_3_deg 19.149 r_dihedral_angle_4_deg 18.156 r_dihedral_angle_1_deg 7.017 r_angle_other_deg 1.932 r_angle_refined_deg 1.807 r_chiral_restr 0.106 r_bond_refined_d 0.013 r_bond_other_d 0.008 r_gen_planes_refined 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.645 r_dihedral_angle_3_deg 19.149 r_dihedral_angle_4_deg 18.156 r_dihedral_angle_1_deg 7.017 r_angle_other_deg 1.932 r_angle_refined_deg 1.807 r_chiral_restr 0.106 r_bond_refined_d 0.013 r_bond_other_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.005 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 11497 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement