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Crystal structure of the isolated H. influenzae VapD toxin (D7N mutant)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZI0 D_1292109585
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 292 50 mM Na cacodylate, 1.8 M ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 2.68 54.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.38 α = 90 b = 84.38 β = 90 c = 49.48 γ = 120
Symmetry Space Group P 3 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-F 2019-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.98021 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.2 42.226 97.2 0.06 0.071 0.999 12.11 3.334 10306 53.573
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 97.9 0.928 1.122 0.612 1.31 3.096
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE D_1292109585 2.2 42.226 10306 1028 97.227 0.22 0.2145 0.2666 0.233 58.862
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] 0.876 0.438 0.876 -2.842
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.923 r_dihedral_angle_4_deg 23.103 r_dihedral_angle_3_deg 20.082 r_lrange_it 17.508 r_lrange_other 17.478 r_scangle_it 9.149 r_scangle_other 9.134 r_mcangle_it 7.78 r_mcangle_other 7.778 r_dihedral_angle_1_deg 7.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.923 r_dihedral_angle_4_deg 23.103 r_dihedral_angle_3_deg 20.082 r_lrange_it 17.508 r_lrange_other 17.478 r_scangle_it 9.149 r_scangle_other 9.134 r_mcangle_it 7.78 r_mcangle_other 7.778 r_dihedral_angle_1_deg 7.316 r_scbond_it 5.796 r_scbond_other 5.773 r_mcbond_it 4.931 r_mcbond_other 4.931 r_angle_refined_deg 1.484 r_angle_other_deg 1.285 r_symmetry_nbd_refined 0.348 r_nbd_other 0.296 r_nbd_refined 0.257 r_xyhbond_nbd_refined 0.226 r_symmetry_xyhbond_nbd_refined 0.218 r_symmetry_nbd_other 0.214 r_nbtor_refined 0.175 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1333 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction