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Structural and biochemical analysis of a prototypical ATPase from the type III secretion system of pathogenic bacteria
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OBL PDB ENTRY 1OBL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 7% (w/v) PEG 8000, 0.1M Calcium Acetate, 0.1M Imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.33 47.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.131 α = 90 b = 78.69 β = 90 c = 53.07 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 105 IMAGE PLATE MAR scanner 345 mm plate M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5428
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 2.25 50 98.8 0.06 36.3 8.6 17405 17196
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 2.25 2.33 97.1 0.379 5.23 8.1 1704
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1OBL 2.25 20 16475 16271 867 98.76 0.21088 0.20817 0.2063 0.26329 0.2541 RANDOM 32.775
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] -1.39 -0.51 1.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.778 r_dihedral_angle_4_deg 19.792 r_dihedral_angle_3_deg 16.196 r_dihedral_angle_1_deg 5.553 r_mcangle_it 1.643 r_scangle_it 1.381 r_angle_refined_deg 1.181 r_mcbond_it 0.982 r_scbond_it 0.871 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.778 r_dihedral_angle_4_deg 19.792 r_dihedral_angle_3_deg 16.196 r_dihedral_angle_1_deg 5.553 r_mcangle_it 1.643 r_scangle_it 1.381 r_angle_refined_deg 1.181 r_mcbond_it 0.982 r_scbond_it 0.871 r_nbtor_refined 0.315 r_symmetry_hbond_refined 0.283 r_symmetry_vdw_refined 0.238 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.202 r_chiral_restr 0.077 r_symmetry_metal_ion_refined 0.043 r_metal_ion_refined 0.026 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2595 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling