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Crystal structure of Haemophilus Influenzae BamA POTRA1-4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6IZS 6IZS, 2QDF experimental model PDB 2QDF 6IZS, 2QDF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 potassium sodium tartrate
Crystal Properties Matthews coefficient Solvent content 4.37 71.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.34 α = 90 b = 127.34 β = 90 c = 136.84 γ = 120
Symmetry Space Group P 62 2 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 CCD MAR CCD 130 mm 2017-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9793 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3 58.1 99.9 0.198 0.99 14.2 25.3 13673
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 3 3.11 0.03 0.54
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 6IZS, 2QDF 3 58.1 12972 682 99.85 0.19386 0.19085 0.1999 0.25172 0.2545 RANDOM 111.8
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] 1.28 0.64 1.28 -4.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.599 r_dihedral_angle_3_deg 23.419 r_dihedral_angle_4_deg 23.183 r_long_range_B_refined 17.056 r_long_range_B_other 17.025 r_scangle_other 12.852 r_dihedral_angle_1_deg 11.971 r_mcangle_it 11.495 r_mcangle_other 11.491 r_scbond_other 8.211
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.599 r_dihedral_angle_3_deg 23.419 r_dihedral_angle_4_deg 23.183 r_long_range_B_refined 17.056 r_long_range_B_other 17.025 r_scangle_other 12.852 r_dihedral_angle_1_deg 11.971 r_mcangle_it 11.495 r_mcangle_other 11.491 r_scbond_other 8.211 r_scbond_it 8.209 r_mcbond_other 7.599 r_mcbond_it 7.598 r_angle_refined_deg 2.449 r_angle_other_deg 1.149 r_chiral_restr 0.129 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2552 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing