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Crystal structure of outer membrane expressed Chitoporin VhChip from Vibrio harveyi in complex with chitotetraose
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 4.31 71.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 250.01 α = 90 b = 145.047 β = 94.8 c = 55.158 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 2015-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979490 Diamond I04
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 2.6 125.35 93.4 0.09 0.081 8.4 2.9 56059
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.68 95.1 0.777 0.699 1.1 2.9
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 2.6 125.35 54404 1652 93.15 0.22201 0.22126 0.2247 0.24749 0.2466 RANDOM 62.644
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] 2.3 -1.36 -0.79 -1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.634 r_dihedral_angle_4_deg 17.162 r_dihedral_angle_3_deg 15.183 r_dihedral_angle_1_deg 7.721 r_long_range_B_other 3.825 r_long_range_B_refined 3.823 r_scangle_other 2.699 r_angle_refined_deg 2.085 r_scbond_other 1.752 r_scbond_it 1.751
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.634 r_dihedral_angle_4_deg 17.162 r_dihedral_angle_3_deg 15.183 r_dihedral_angle_1_deg 7.721 r_long_range_B_other 3.825 r_long_range_B_refined 3.823 r_scangle_other 2.699 r_angle_refined_deg 2.085 r_scbond_other 1.752 r_scbond_it 1.751 r_mcangle_it 1.578 r_mcangle_other 1.578 r_angle_other_deg 1.038 r_mcbond_it 0.962 r_mcbond_other 0.962 r_chiral_restr 0.109 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 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 7995 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 171
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing