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Crystal structure of the Loop 7 mutant PorB from Neisseria meningitidis serogroup B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VZT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 65mM HEPES pH 7.5, 1.1M tri-sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.486 α = 90 b = 143.486 β = 90 c = 178.42 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 PILATUS 2M 2012-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 50 92.2 25466 17.4 1.55
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.45 73
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 3VZT 2.4 50 23673 1791 91.9 0.22946 0.22745 0.2233 0.25596 0.2526 RANDOM 51.113
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] -1.15 -0.57 -1.15 1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.25 r_dihedral_angle_4_deg 19.203 r_dihedral_angle_3_deg 15.615 r_dihedral_angle_1_deg 7.052 r_angle_refined_deg 1.638 r_chiral_restr 0.117 r_bond_refined_d 0.016 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2393 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 26
Software Software Software Name Purpose HKL-2000 data collection MLPHARE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASES phasing