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Crystal structure of the VirB11 ATPase from the Brucella Suis type IV secretion system in complex with sulphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OPX PDB entry 1OPX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.8 293 16% PEG 4000, 0.1M Tris HCl, 0.2M lithium sulphate, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.49 50.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.211 α = 90 b = 125.815 β = 90 c = 164.089 γ = 90
Symmetry Space Group C 2 2 21
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 QUANTUM 4 2004-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.97870 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.6 29.709 98 0.068 0.068 8.5 7.4 37793 37055 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.74 97.5 0.284 0.284 2.7 7.3 5314
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 (All) 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 1OPX 2.6 29.709 37793 37050 3746 97.73 0.242 0.242 0.238 0.2362 0.279 0.2784 RANDOM 40.445
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] 1.64 1.72 -3.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.442 r_dihedral_angle_4_deg 21.012 r_dihedral_angle_3_deg 18.448 r_dihedral_angle_1_deg 5.056 r_scangle_it 1.497 r_angle_refined_deg 1.479 r_scbond_it 0.847 r_mcangle_it 0.651 r_mcbond_it 0.437 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.442 r_dihedral_angle_4_deg 21.012 r_dihedral_angle_3_deg 18.448 r_dihedral_angle_1_deg 5.056 r_scangle_it 1.497 r_angle_refined_deg 1.479 r_scbond_it 0.847 r_mcangle_it 0.651 r_mcbond_it 0.437 r_nbtor_refined 0.309 r_symmetry_hbond_refined 0.226 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.2 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7569 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 15
Software Software Software Name Purpose EPMR phasing ADSC data collection CCP4 data scaling REFMAC refinement