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Crystal structure of the isolated H. influenzae VapD toxin (wildtype)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HKD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 292 1 M LiCl, 0.1 M citrate, 20% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.66 53.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.1 α = 90 b = 99.1 β = 90 c = 44.47 γ = 120
Symmetry Space Group P 63 2 2
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 2019-03-22 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 2.5 85.882 99.9 0.212 0.223 0.996 9.49 10.357 4800 44.739
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 2.5 2.56 100 1.581 1.659 0.546 1.33 10.677
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 6HKD 2.5 85.882 4800 241 99.917 0.222 0.2202 0.2345 0.2636 0.283 76.248
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] 0.869 0.435 0.869 -2.821
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.995 r_dihedral_angle_4_deg 25.709 r_dihedral_angle_3_deg 18.109 r_lrange_it 16.647 r_lrange_other 16.564 r_scangle_it 11.133 r_scangle_other 11.13 r_mcangle_other 9.815 r_mcangle_it 9.803 r_dihedral_angle_1_deg 8.513
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.995 r_dihedral_angle_4_deg 25.709 r_dihedral_angle_3_deg 18.109 r_lrange_it 16.647 r_lrange_other 16.564 r_scangle_it 11.133 r_scangle_other 11.13 r_mcangle_other 9.815 r_mcangle_it 9.803 r_dihedral_angle_1_deg 8.513 r_scbond_it 7.744 r_scbond_other 7.435 r_mcbond_it 6.859 r_mcbond_other 6.646 r_angle_refined_deg 1.741 r_angle_other_deg 1.24 r_symmetry_xyhbond_nbd_refined 0.256 r_symmetry_nbd_refined 0.255 r_nbd_other 0.238 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.201 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.167 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 722 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction PHASER phasing XSCALE data scaling