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Structure of OmpF co-crystallized with T83
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OMF
Crystallization Crystal Properties Matthews coefficient Solvent content 2.99 58.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.867 α = 90 b = 116.867 β = 90 c = 114.331 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 2007-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97935 APS 19-ID
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 3 99.9 0.076 8.3 17885 -3
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 3 101.02 16925 896 99.96 0.26697 0.26555 0.2628 0.29392 0.2909 RANDOM 48.67
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] -5.38 -2.69 -5.38 8.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.323 r_dihedral_angle_3_deg 15.309 r_dihedral_angle_4_deg 5.907 r_dihedral_angle_1_deg 5.454 r_angle_refined_deg 0.976 r_scangle_it 0.748 r_mcangle_it 0.729 r_scbond_it 0.471 r_mcbond_it 0.4 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.323 r_dihedral_angle_3_deg 15.309 r_dihedral_angle_4_deg 5.907 r_dihedral_angle_1_deg 5.454 r_angle_refined_deg 0.976 r_scangle_it 0.748 r_mcangle_it 0.729 r_scbond_it 0.471 r_mcbond_it 0.4 r_nbtor_refined 0.301 r_nbd_refined 0.183 r_symmetry_hbond_refined 0.157 r_symmetry_vdw_refined 0.148 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 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_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 5294 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction SCALEPACK data scaling MOLREP phasing