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Cation selective pathway of OmpF porin revealed by anomalous x-ray diffraction
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OMF PDB entry 2OMF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.5M NaCl, Na Phosphate pH 6.5, 0.9% BOG, 0.09% octylPOE and 14-18% PEG2000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.07 59.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.545 α = 90 b = 117.545 β = 90 c = 121.287 γ = 120
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 315 2007-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B
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 2.61 50 89.2 0.147 28.9 6.8 26020
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) 2.61 2.69 74.5 0.4 5.51 4 2154
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 PDB entry 2OMF 2.61 46.93 24470 1323 89.12 0.23246 0.22876 0.2257 0.30028 0.2238 RANDOM 51.921
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] -5.72 -2.86 -5.72 8.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.343 r_dihedral_angle_4_deg 21.013 r_dihedral_angle_3_deg 19.016 r_dihedral_angle_1_deg 8.754 r_scangle_it 6.394 r_scbond_it 4.198 r_angle_refined_deg 2.795 r_mcangle_it 2.55 r_mcbond_it 1.443 r_nbtor_refined 0.329
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.343 r_dihedral_angle_4_deg 21.013 r_dihedral_angle_3_deg 19.016 r_dihedral_angle_1_deg 8.754 r_scangle_it 6.394 r_scbond_it 4.198 r_angle_refined_deg 2.795 r_mcangle_it 2.55 r_mcbond_it 1.443 r_nbtor_refined 0.329 r_nbd_refined 0.279 r_metal_ion_refined 0.244 r_symmetry_hbond_refined 0.212 r_xyhbond_nbd_refined 0.208 r_symmetry_vdw_refined 0.203 r_chiral_restr 0.177 r_bond_refined_d 0.037 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other 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 5238 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 44
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling