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Structure of the head of the Bartonella adhesin BadA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S7M PDB ENTRY 1s7m
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 0.05M ammonium sulfate, 0.05M Bis-Tris (pH 6.5), 30% v/v pentaerythrol ethoxylate, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.538955 20.075651
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.87 α = 65.87 b = 51.14 β = 76.6 c = 58.62 γ = 82.08
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 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1 ESRF ID29
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 1.13 30 90.7 0.085 3.7 5.8 105179 3.7 13.6
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) 1.13 1.16 76 0.52 3.7 5.4 14273
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 1s7m 1.13 25 105179 99858 5256 100 0.157 0.15704 0.15592 0.1613 0.17801 0.1812 RANDOM 10.076
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] 0.1 0.22 -0.15 -0.09 0.23 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.2 r_dihedral_angle_4_deg 27.203 r_dihedral_angle_3_deg 11.182 r_dihedral_angle_1_deg 6.177 r_sphericity_free 4.429 r_scangle_it 3.419 r_scbond_it 2.623 r_sphericity_bonded 2.521 r_mcangle_it 2.005 r_mcbond_it 1.769
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.2 r_dihedral_angle_4_deg 27.203 r_dihedral_angle_3_deg 11.182 r_dihedral_angle_1_deg 6.177 r_sphericity_free 4.429 r_scangle_it 3.419 r_scbond_it 2.623 r_sphericity_bonded 2.521 r_mcangle_it 2.005 r_mcbond_it 1.769 r_angle_refined_deg 1.369 r_rigid_bond_restr 1.345 r_angle_other_deg 0.829 r_mcbond_other 0.471 r_symmetry_vdw_refined 0.226 r_symmetry_hbond_refined 0.215 r_nbd_refined 0.211 r_nbd_other 0.191 r_symmetry_vdw_other 0.188 r_nbtor_refined 0.161 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.084 r_nbtor_other 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2584 Nucleic Acid Atoms Solvent Atoms 422 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection XDS data reduction XSCALE data scaling MOLREP phasing