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OmpT (in-vitro folded), an outer membrane protein Vibrio cholerae (trimer form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EHD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.2 298 0.05 M calcium chloride dihydrate, 0.05 M barium chloride, 0.1 M tris, 32% PEG 400
Crystal Properties Matthews coefficient Solvent content 4.45 72.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 200.91 α = 90 b = 200.91 β = 90 c = 200.91 γ = 90
Symmetry Space Group I 4 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 PIXEL DECTRIS PILATUS 6M-F 2016-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9762 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) 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 2.72 71.03 99 0.025 1 22.1 42.2 18714
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 2.72 98 0.679 0.6 1.2 43.7
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 6EHD 2.72 71.03 17747 956 98.98 0.24015 0.23798 0.2398 0.28059 0.2866 RANDOM 96.065
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 38.924 r_dihedral_angle_4_deg 26.628 r_dihedral_angle_3_deg 17.646 r_long_range_B_refined 13.903 r_long_range_B_other 13.901 r_scangle_other 11.67 r_mcangle_it 10.552 r_mcangle_other 10.549 r_dihedral_angle_1_deg 9.045 r_scbond_it 8.333
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.924 r_dihedral_angle_4_deg 26.628 r_dihedral_angle_3_deg 17.646 r_long_range_B_refined 13.903 r_long_range_B_other 13.901 r_scangle_other 11.67 r_mcangle_it 10.552 r_mcangle_other 10.549 r_dihedral_angle_1_deg 9.045 r_scbond_it 8.333 r_scbond_other 8.333 r_mcbond_it 7.629 r_mcbond_other 7.629 r_angle_refined_deg 1.91 r_angle_other_deg 1.036 r_chiral_restr 0.109 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 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 2451 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing