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OmpU, an outer membrane protein, of Vibrio cholerae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UPG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.2 M sodium acetate, 0.1 M MES, 28% w/v 400 PEG
Crystal Properties Matthews coefficient Solvent content 2.9 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.723 α = 90 b = 153.84 β = 102.32 c = 66.17 γ = 90
Symmetry Space Group P 1 21 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 2014-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97949 Diamond I03
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 1.55 49.49 97 0.037 0.9 9.8 3.9 171689
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 1.55 95 0.555 0.5 1.4 4
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 3UPG 1.55 49.49 163191 8445 97.11 0.17172 0.17029 0.1819 0.19929 0.2069 RANDOM 23.584
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] 0.81 -0.03 -0.45 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.847 r_dihedral_angle_4_deg 15.589 r_dihedral_angle_3_deg 11.967 r_dihedral_angle_1_deg 6.796 r_long_range_B_refined 6.559 r_long_range_B_other 6.559 r_scangle_other 5.284 r_scbond_it 3.566 r_scbond_other 3.565 r_mcangle_it 3.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.847 r_dihedral_angle_4_deg 15.589 r_dihedral_angle_3_deg 11.967 r_dihedral_angle_1_deg 6.796 r_long_range_B_refined 6.559 r_long_range_B_other 6.559 r_scangle_other 5.284 r_scbond_it 3.566 r_scbond_other 3.565 r_mcangle_it 3.119 r_mcangle_other 3.119 r_mcbond_it 2.285 r_mcbond_other 2.284 r_angle_refined_deg 2.149 r_angle_other_deg 1.046 r_chiral_restr 0.134 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 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 7301 Nucleic Acid Atoms Solvent Atoms 639 Heterogen Atoms 202
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing