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Crystal Structure of outer membrane protein PorB with G103K mutations from Neisseria meningitidis W135
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VY8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 100 mM MES, pH 6.5
31% Jeffamine M-600
Crystal Properties Matthews coefficient Solvent content 2.99 58.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.396 α = 90 b = 84.396 β = 90 c = 107.11 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 100 PIXEL DECTRIS PILATUS3 6M 2014-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.75 43.3 99.8 0.077 22.6 6.7 11223
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.81 0.84
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3VY8 2.76 43.237 11178 564 99.795 0.216 0.2132 0.2163 0.2603 0.2605 90.754
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] 3.893 1.946 3.893 -12.628
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.718 r_dihedral_angle_3_deg 17.112 r_lrange_it 13.475 r_lrange_other 13.473 r_dihedral_angle_4_deg 11.81 r_scangle_it 10.191 r_scangle_other 10.191 r_mcangle_it 8.916 r_mcangle_other 8.915 r_dihedral_angle_1_deg 7.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.718 r_dihedral_angle_3_deg 17.112 r_lrange_it 13.475 r_lrange_other 13.473 r_dihedral_angle_4_deg 11.81 r_scangle_it 10.191 r_scangle_other 10.191 r_mcangle_it 8.916 r_mcangle_other 8.915 r_dihedral_angle_1_deg 7.77 r_scbond_it 6.696 r_scbond_other 6.696 r_mcbond_it 6.182 r_mcbond_other 6.179 r_angle_other_deg 1.509 r_angle_refined_deg 1.466 r_nbd_other 0.254 r_symmetry_nbd_refined 0.239 r_symmetry_nbd_other 0.213 r_nbd_refined 0.191 r_symmetry_xyhbond_nbd_refined 0.183 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.152 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.067 r_symmetry_xyhbond_nbd_other 0.062 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2598 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling REFMAC phasing