☰ Navigation Tabs
Crystal structure of the C. difficile toxin A CROPs domain fragment 2592-2710 bound to H5.2 nanobody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F6E experimental model PDB 6DBA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 288 0.2M Ammonium phosphate dibasic, pH 8.0, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.99 38.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.156 α = 90 b = 71.739 β = 90 c = 93.405 γ = 90
Symmetry Space Group P 21 21 21
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 RIGAKU HyPix-6000HE 2023-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU PhotonJet-S 1.5418
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 1.65 21.35 98.5 0.03 0.032 0.009 1 54.1 11.1 26488
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 1.65 1.68 82.3 0.107 0.121 0.055 0.983 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.65 21.35 25128 1304 98.51 0.15108 0.14871 0.19836 0.1886 RANDOM 11.363
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] 0.11 -0.12 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.689 r_dihedral_angle_2_deg 9.175 r_dihedral_angle_1_deg 6.852 r_long_range_B_refined 4.977 r_scbond_it 2.189 r_angle_refined_deg 2.04 r_mcangle_it 1.926 r_mcbond_it 1.196 r_chiral_restr 0.145 r_gen_planes_refined 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.689 r_dihedral_angle_2_deg 9.175 r_dihedral_angle_1_deg 6.852 r_long_range_B_refined 4.977 r_scbond_it 2.189 r_angle_refined_deg 2.04 r_mcangle_it 1.926 r_mcbond_it 1.196 r_chiral_restr 0.145 r_gen_planes_refined 0.012 r_bond_refined_d 0.011 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1883 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement Aimless data scaling CrysalisPro data reduction MoRDa phasing