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Outer membrane protein assembly factor BamB from Klebsiella pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PRW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 22% PEG 400, 0.1 M sodium acetate trihydrate (pH 4.6) and 0.08 M cadmium acetate trihydrate
Crystal Properties Matthews coefficient Solvent content 2.1 41.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.095 α = 90 b = 50.095 β = 90 c = 259.774 γ = 90
Symmetry Space Group P 43 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 100 PIXEL DECTRIS PILATUS 2M 2017-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9282 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.57 29.285 99.8 0.073 1 25.6 24 48078
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.57 1.61 97.7 0.665 0.92 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.68 29.285 39184 1954 99.964 0.173 0.1711 0.1818 0.2098 0.2176 22.911
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] 0.191 0.191 -0.382
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.281 r_dihedral_angle_3_deg 12.696 r_dihedral_angle_4_deg 12.011 r_dihedral_angle_1_deg 7.215 r_lrange_it 5.745 r_lrange_other 5.536 r_scangle_it 2.952 r_scangle_other 2.951 r_mcangle_it 2.392 r_mcangle_other 2.392
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.281 r_dihedral_angle_3_deg 12.696 r_dihedral_angle_4_deg 12.011 r_dihedral_angle_1_deg 7.215 r_lrange_it 5.745 r_lrange_other 5.536 r_scangle_it 2.952 r_scangle_other 2.951 r_mcangle_it 2.392 r_mcangle_other 2.392 r_scbond_it 1.856 r_scbond_other 1.855 r_mcbond_it 1.45 r_mcbond_other 1.43 r_angle_refined_deg 1.426 r_angle_other_deg 1.271 r_symmetry_nbd_refined 0.274 r_nbd_refined 0.188 r_xyhbond_nbd_refined 0.188 r_metal_ion_refined 0.176 r_symmetry_nbd_other 0.17 r_nbd_other 0.163 r_nbtor_refined 0.144 r_symmetry_xyhbond_nbd_refined 0.137 r_symmetry_nbtor_other 0.07 r_chiral_restr 0.058 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2631 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing