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Crystal Structure of the RdfS Excisionase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold alphafold prediction
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.05 M MES; pH 6.5, 4% w/v PEG 5000 MME, 5% v/v 1-propanol, 0.1 M sodium citrate; RdfS protein at 4.3 mg/mL
Crystal Properties Matthews coefficient Solvent content 3.25 62.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.251 α = 90 b = 119.204 β = 90 c = 123.397 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 EIGER X 16M 2021-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953 Australian Synchrotron MX2
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 2.45 42.87 99.4 0.142 0.155 0.06 0.993 9 6.6 19949 41.59
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 2.45 2.55 94.7 0.855 0.927 0.354 0.744 6.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 alphafold prediction 2.45 42.87 1.34 19891 933 99.39 0.2015 0.1993 0.1996 0.2456 0.2451 Random selection 44.7947
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2160 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 22
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing MOLREP phasing PDB_EXTRACT data extraction