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Crystal structure of Haemophilus influenzae BamA POTRA4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QDF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.81 67.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.53 α = 90 b = 80.53 β = 90 c = 105.141 γ = 120
Symmetry Space Group P 65 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 165 mm 2017-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NFPSS BEAMLINE BL19U1 0.9785 NFPSS BL19U1
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 2.03 42 99.8 0.12 0.99 21.6 35.1 13557
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.03 2.1 99.7 1.77 1.77 0.75
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 2QDF 2.03 42 12912 640 99.62 0.17999 0.17828 0.1932 0.21765 0.2233 RANDOM 57.09
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] 0.15 0.07 0.15 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.629 r_dihedral_angle_4_deg 19.271 r_dihedral_angle_3_deg 17.698 r_long_range_B_refined 10.552 r_long_range_B_other 10.463 r_scangle_other 8.251 r_dihedral_angle_1_deg 6.411 r_scbond_it 5.551 r_scbond_other 5.543 r_mcangle_it 5.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.629 r_dihedral_angle_4_deg 19.271 r_dihedral_angle_3_deg 17.698 r_long_range_B_refined 10.552 r_long_range_B_other 10.463 r_scangle_other 8.251 r_dihedral_angle_1_deg 6.411 r_scbond_it 5.551 r_scbond_other 5.543 r_mcangle_it 5.144 r_mcangle_other 5.138 r_mcbond_other 3.713 r_mcbond_it 3.709 r_angle_refined_deg 2.909 r_angle_other_deg 1.374 r_chiral_restr 0.162 r_bond_refined_d 0.032 r_gen_planes_refined 0.012 r_bond_other_d 0.003 r_gen_planes_other 0.001 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 656 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing