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The Structure of OmpF porin with a synthetic dibenzo-18-crown-6 as modulator
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OMF 2OMF with K16 mutated to alanine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 291 0.2 M CaCl2, 48% PEG 400, 0.1 M Na-HEPES, pH 7.5, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.4 63.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.52 α = 90 b = 135.52 β = 90 c = 47.52 γ = 120
Symmetry Space Group P 3 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 CCD ADSC QUANTUM 315r 2008-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.934 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 3.4 44.36 98.8 0.17 0.17 9.5 5.4 7096 6991 0.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.4 3.6 97.2 0.274 0.274 5 4
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 2OMF with K16 mutated to alanine 3.4 44.36 6601 388 98.45 0.25152 0.2491 0.2488 0.29437 0.2913 RANDOM 54.37
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] 1.55 0.77 1.55 -2.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.842 r_dihedral_angle_3_deg 17.694 r_dihedral_angle_4_deg 16.534 r_dihedral_angle_1_deg 6.552 r_angle_other_deg 3.005 r_angle_refined_deg 1.3 r_scangle_it 1.041 r_mcangle_it 0.745 r_scbond_it 0.732 r_mcbond_it 0.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.842 r_dihedral_angle_3_deg 17.694 r_dihedral_angle_4_deg 16.534 r_dihedral_angle_1_deg 6.552 r_angle_other_deg 3.005 r_angle_refined_deg 1.3 r_scangle_it 1.041 r_mcangle_it 0.745 r_scbond_it 0.732 r_mcbond_it 0.412 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.24 r_nbd_refined 0.227 r_symmetry_hbond_refined 0.218 r_xyhbond_nbd_refined 0.189 r_nbd_other 0.156 r_nbtor_other 0.103 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_bond_other_d 0.003 r_gen_planes_refined 0.003 r_gen_planes_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2624 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 45
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling