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Structural insights of the outer-membrane channel OprN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D5K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1 M Sodium acetate pH 5.4, 0.8 M Sodium formate, 11% PEG 4000
Crystal Properties Matthews coefficient Solvent content 4.55 72.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 257.648 α = 90 b = 257.648 β = 90 c = 81.511 γ = 90
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 PILATUS3 2M 2015-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
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 2.29 182.185 99.4 0.149 8.04 4.88 119764
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 2.29 2.37 99.5 0.755 1.76 4.49
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 FREE R-VALUE 3D5K 2.29 182.18 113747 6012 99.39 0.18993 0.18805 0.1957 0.22536 0.229 RANDOM 35.643
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.333 r_dihedral_angle_4_deg 21.82 r_dihedral_angle_3_deg 15.906 r_long_range_B_other 8.569 r_long_range_B_refined 8.565 r_scangle_other 6.856 r_dihedral_angle_1_deg 5.911 r_scbond_it 4.592 r_scbond_other 4.592 r_mcangle_it 4.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.333 r_dihedral_angle_4_deg 21.82 r_dihedral_angle_3_deg 15.906 r_long_range_B_other 8.569 r_long_range_B_refined 8.565 r_scangle_other 6.856 r_dihedral_angle_1_deg 5.911 r_scbond_it 4.592 r_scbond_other 4.592 r_mcangle_it 4.009 r_mcangle_other 4.009 r_mcbond_it 2.988 r_mcbond_other 2.988 r_angle_refined_deg 2.074 r_angle_other_deg 1.085 r_chiral_restr 0.105 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 10316 Nucleic Acid Atoms Solvent Atoms 681 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing