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H/L (SLPH/SLPL) complex from C. difficile (CD630 strain)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CVZ 3CVZ, 5j6Q, D_129211090/992/994 experimental model PDB 5J6Q 3CVZ, 5j6Q, D_129211090/992/994
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 293 0.1 M MES pH 6.2
1.25 Lithium chloride
16% PEG 6000
10% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.63 53.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.67 α = 81.89 b = 78.25 β = 66.98 c = 81.58 γ = 65.26
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 2018-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.55 52.31 96.4 0.128 0.153 0.083 0.992 7 3.3 47230 60.17
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.64 97.6 0.704 0.836 0.445 0.732 1.5 3.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3CVZ, 5j6Q, D_129211090/992/994 2.55 52.31 44767 2432 96.4 0.23 0.23 0.2327 0.26 0.2597 RANDOM 60.166
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] -1.1 0.68 -0.19 1.05 0.54 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.645 r_dihedral_angle_4_deg 18.464 r_dihedral_angle_3_deg 12.727 r_dihedral_angle_1_deg 4.699 r_long_range_B_refined 3.531 r_long_range_B_other 3.53 r_mcangle_it 1.788 r_mcangle_other 1.788 r_scangle_other 1.415 r_mcbond_it 1.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.645 r_dihedral_angle_4_deg 18.464 r_dihedral_angle_3_deg 12.727 r_dihedral_angle_1_deg 4.699 r_long_range_B_refined 3.531 r_long_range_B_other 3.53 r_mcangle_it 1.788 r_mcangle_other 1.788 r_scangle_other 1.415 r_mcbond_it 1.005 r_mcbond_other 1.005 r_angle_other_deg 0.917 r_angle_refined_deg 0.916 r_scbond_it 0.808 r_scbond_other 0.796 r_chiral_restr 0.05 r_bond_refined_d 0.004 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10306 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing