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Crystal structure of sliding beta clamp from Helicobacter pylori
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AWA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 289 6% Peg20000, 20% Peg550MME, 0.1M Hepes+MOPS pH7.3, 0.2M Ammonium citrate dibasic, 10mM MgCl2+10mM SrCl2, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.54 51.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.534 α = 90 b = 65.886 β = 115.79 c = 82.723 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 100 IMAGE PLATE MAR scanner 345 mm plate 2014-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.769 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.05 50 99.5 0.06 29.43 3.8 52832 -3 39.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.09 95 0.54 2.05 3.5 2442
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 MR SAD THROUGHOUT 2AWA 2.05 50 52832 25673 1358 98.56 0.21658 0.2149 0.2221 0.24729 0.2566 RANDOM 53.213
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] 3.16 1.33 -5.05 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.807 r_dihedral_angle_4_deg 13.69 r_dihedral_angle_3_deg 13.664 r_dihedral_angle_1_deg 6.385 r_long_range_B_refined 5.733 r_long_range_B_other 5.719 r_scangle_other 3.287 r_mcangle_it 2.864 r_mcangle_other 2.864 r_scbond_it 2.042
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.807 r_dihedral_angle_4_deg 13.69 r_dihedral_angle_3_deg 13.664 r_dihedral_angle_1_deg 6.385 r_long_range_B_refined 5.733 r_long_range_B_other 5.719 r_scangle_other 3.287 r_mcangle_it 2.864 r_mcangle_other 2.864 r_scbond_it 2.042 r_scbond_other 2.041 r_mcbond_it 1.801 r_mcbond_other 1.801 r_angle_refined_deg 1.136 r_angle_other_deg 0.678 r_chiral_restr 0.064 r_bond_refined_d 0.006 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 2967 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms
Software Software Software Name Purpose DNA data collection PHENIX model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing