☰ Navigation Tabs
Crystal structure of outer membrane expressed Chitoporin VhChip from Vibrio harveyi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MDO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 28% (w/v) PEG 400,
0.2 M sodium acetate,
0.1 M MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 4.45 72.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 255.73 α = 90 b = 148.639 β = 94.94 c = 54.364 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 100 PIXEL DECTRIS PILATUS 6M 2014-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.92 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.5 49.15 95.5 0.086 0.078 12.2 4.1 66687
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 5MDO 2.5 128.39 64598 2089 95.4 0.23048 0.23013 0.2329 0.24093 0.2415 RANDOM 55.574
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] -1.2 0.48 0.59 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.813 r_dihedral_angle_4_deg 19.92 r_dihedral_angle_3_deg 15.443 r_dihedral_angle_1_deg 7.281 r_long_range_B_refined 3.272 r_long_range_B_other 3.251 r_scangle_other 2.006 r_angle_refined_deg 1.923 r_mcangle_it 1.538 r_mcangle_other 1.538
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.813 r_dihedral_angle_4_deg 19.92 r_dihedral_angle_3_deg 15.443 r_dihedral_angle_1_deg 7.281 r_long_range_B_refined 3.272 r_long_range_B_other 3.251 r_scangle_other 2.006 r_angle_refined_deg 1.923 r_mcangle_it 1.538 r_mcangle_other 1.538 r_angle_other_deg 1.362 r_scbond_it 1.226 r_scbond_other 1.226 r_mcbond_it 0.921 r_mcbond_other 0.921 r_chiral_restr 0.116 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.009 r_gen_planes_other 0.007 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 8169 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing