☰ Navigation Tabs
OmpT (in-vitro folded), an outer membrane protein of Vibrio cholerae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EHB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.1 M NaCl, 0.1 M MES, 33% v/v PEG 400, 4% v/v ethylene glycol
Crystal Properties Matthews coefficient Solvent content 3.46 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.88 α = 90 b = 75.84 β = 92.06 c = 49.67 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 2016-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9282 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 1.66 49.64 99 0.022 0.9 14.5 3.4 62456
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 1.66 97.9 0.61 0.5 1.1 2.5
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 6EHB 1.66 49.64 59541 2915 99.13 0.18772 0.18648 0.1996 0.21397 0.2259 RANDOM 39.331
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] 3.12 -0.63 -1.49 -1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.626 r_dihedral_angle_4_deg 17.782 r_dihedral_angle_3_deg 14.299 r_long_range_B_refined 9.543 r_long_range_B_other 9.485 r_dihedral_angle_1_deg 7.536 r_scangle_other 7.146 r_mcangle_it 5.556 r_mcangle_other 5.556 r_scbond_it 4.921
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.626 r_dihedral_angle_4_deg 17.782 r_dihedral_angle_3_deg 14.299 r_long_range_B_refined 9.543 r_long_range_B_other 9.485 r_dihedral_angle_1_deg 7.536 r_scangle_other 7.146 r_mcangle_it 5.556 r_mcangle_other 5.556 r_scbond_it 4.921 r_scbond_other 4.91 r_mcbond_it 4.172 r_mcbond_other 4.165 r_angle_refined_deg 2.185 r_angle_other_deg 1.063 r_chiral_restr 0.147 r_bond_refined_d 0.024 r_gen_planes_refined 0.011 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 2489 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 147
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing