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OmpUdeltaN (N-terminus deletion mutant of OmpU), 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, SITTING DROP 9 298 33% PEG 300, 0.1 M NaCl, 0.05 M bicine
Crystal Properties Matthews coefficient Solvent content 2.71 54.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.36 α = 90 b = 81.36 β = 90 c = 198.5 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 298 PIXEL DECTRIS PILATUS 6M-F 2017-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.920 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.02 57.52 100 0.9 12.3 11.5 48646
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 2.02 100 0.6 1.3 11.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6EHB 2.02 57.52 46172 2419 99.97 0.19533 0.1926 0.24761 0.2355 RANDOM 39.774
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] -1.74 -0.87 -1.74 5.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.655 r_dihedral_angle_4_deg 16.4 r_dihedral_angle_3_deg 14.124 r_long_range_B_refined 7.164 r_long_range_B_other 7.164 r_dihedral_angle_1_deg 6.967 r_scangle_other 5.392 r_mcangle_it 4.209 r_mcangle_other 4.209 r_scbond_it 3.636
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.655 r_dihedral_angle_4_deg 16.4 r_dihedral_angle_3_deg 14.124 r_long_range_B_refined 7.164 r_long_range_B_other 7.164 r_dihedral_angle_1_deg 6.967 r_scangle_other 5.392 r_mcangle_it 4.209 r_mcangle_other 4.209 r_scbond_it 3.636 r_scbond_other 3.636 r_mcbond_it 3.011 r_mcbond_other 3.009 r_angle_refined_deg 1.652 r_angle_other_deg 0.943 r_chiral_restr 0.109 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 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 4714 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing