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Outer-membrane expressed OmpT of Vibrio cholerae
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 4.5 298 15% PEG 4000
0.1 M sodium acetate
0.4 M ammonium thiocyanate
Crystal Properties Matthews coefficient Solvent content 4.37 72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.61 α = 90 b = 74.33 β = 96.74 c = 62.31 γ = 90
Symmetry Space Group C 1 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 298 PIXEL DECTRIS PILATUS 6M-F 2016-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.979 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.2 46.41 98 5 3.6 6356
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 96 0.5 1.5 3.5
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 3.2 46.41 6206 323 59.26 0.21381 0.21227 0.2186 0.24435 0.2418 RANDOM 77.525
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] -2.57 -1.21 -2.68 5.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.718 r_dihedral_angle_3_deg 19.983 r_long_range_B_refined 11.335 r_long_range_B_other 11.333 r_dihedral_angle_1_deg 8.927 r_dihedral_angle_4_deg 7.914 r_mcangle_it 7.654 r_mcangle_other 7.651 r_scangle_other 6.921 r_mcbond_other 4.587
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.718 r_dihedral_angle_3_deg 19.983 r_long_range_B_refined 11.335 r_long_range_B_other 11.333 r_dihedral_angle_1_deg 8.927 r_dihedral_angle_4_deg 7.914 r_mcangle_it 7.654 r_mcangle_other 7.651 r_scangle_other 6.921 r_mcbond_other 4.587 r_mcbond_it 4.586 r_scbond_it 4.106 r_scbond_other 4.106 r_angle_refined_deg 1.528 r_angle_other_deg 0.93 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2467 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing