☰ Navigation Tabs
X-ray structure of autolysin Acd24020 catalytic domain from Clostridium difficile
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H41
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.1 293 200 mM ammonium citrate dibasic, 20% (w/v) polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.32 47.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.44 α = 104.86 b = 55.21 β = 112.64 c = 57.11 γ = 90.06
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 2M 2019-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.56 36.97 99.2 0.044 0.995 9.4 1.7 73725
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.56 1.6 0.05 0.961
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 3H41 1.56 36.97 69608 3667 94.19 0.20108 0.198 0.2071 0.25844 0.2655 RANDOM 26.501
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] 0.19 -0.17 0.3 -0.45 -0.22 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.292 r_dihedral_angle_4_deg 19.316 r_dihedral_angle_3_deg 13.147 r_dihedral_angle_1_deg 7.152 r_rigid_bond_restr 6.451 r_scangle_other 5.463 r_long_range_B_refined 5.348 r_long_range_B_other 5.345 r_scbond_it 4.766 r_scbond_other 4.765
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.292 r_dihedral_angle_4_deg 19.316 r_dihedral_angle_3_deg 13.147 r_dihedral_angle_1_deg 7.152 r_rigid_bond_restr 6.451 r_scangle_other 5.463 r_long_range_B_refined 5.348 r_long_range_B_other 5.345 r_scbond_it 4.766 r_scbond_other 4.765 r_mcangle_it 4.227 r_mcangle_other 4.226 r_mcbond_it 3.684 r_mcbond_other 3.681 r_angle_refined_deg 1.578 r_angle_other_deg 1.45 r_chiral_restr 0.087 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3759 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing