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Klebsiella pneumoniae OmpK36
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OSM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 295 0.08 M Magnesium Acetate tetrahydrate , 0.1 M sodium citrate, 14% w/v 5000 PEG MME
Crystal Properties Matthews coefficient Solvent content 3.37 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 232.316 α = 90 b = 74.511 β = 112.18 c = 90.814 γ = 90
Symmetry Space Group C 1 2 1
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 6M-F 2015-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.979 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.65 107.57 98.5 0.039 11.6 3.8 169933 16.98
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 97.3 0.607 0.689 1.6 3.9
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 1OSM 1.65 107.57 161366 8563 98.52 0.14829 0.14611 0.1595 0.18963 0.2006 RANDOM 29.285
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] -1.49 0.65 -0.52 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.941 r_sphericity_free 35.742 r_dihedral_angle_4_deg 18.711 r_sphericity_bonded 15.522 r_dihedral_angle_3_deg 12.56 r_dihedral_angle_1_deg 6.361 r_long_range_B_refined 5.177 r_long_range_B_other 4.945 r_scangle_other 4.789 r_scbond_other 4.185
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.941 r_sphericity_free 35.742 r_dihedral_angle_4_deg 18.711 r_sphericity_bonded 15.522 r_dihedral_angle_3_deg 12.56 r_dihedral_angle_1_deg 6.361 r_long_range_B_refined 5.177 r_long_range_B_other 4.945 r_scangle_other 4.789 r_scbond_other 4.185 r_scbond_it 4.184 r_mcangle_it 3.745 r_mcangle_other 3.745 r_mcbond_other 3.065 r_mcbond_it 3.064 r_rigid_bond_restr 2.785 r_angle_refined_deg 1.588 r_angle_other_deg 0.939 r_chiral_restr 0.107 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8027 Nucleic Acid Atoms Solvent Atoms 635 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing