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Crystal structure of C. difficile SpoVD in complex with ampicillin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UN1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 15 % PEG 3350, 0.2 M AmSO4, 10 % PropOH, 0.1 M Na Citrate pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.69 54.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.64 α = 90 b = 95.62 β = 90 c = 176.77 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 DECTRIS PILATUS3 6M 2020-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97911 APS 19-ID
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 2.2 49.58 94.6 0.105 0.123 0.063 0.985 7.3 3.5 62415
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 2.2 2.25 96.8 0.5 0.586 0.299 0.859 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 6UN1 2.2 49.58 59183 3192 93.48 0.1891 0.1871 0.1957 0.2252 0.2338 RANDOM 41.966
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] -3.23 1.2 2.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.918 r_dihedral_angle_3_deg 16.096 r_dihedral_angle_4_deg 15.13 r_dihedral_angle_1_deg 7.123 r_angle_refined_deg 1.518 r_angle_other_deg 1.216 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.918 r_dihedral_angle_3_deg 16.096 r_dihedral_angle_4_deg 15.13 r_dihedral_angle_1_deg 7.123 r_angle_refined_deg 1.518 r_angle_other_deg 1.216 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7855 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 141
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction MOSFLM data reduction MoRDa phasing