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XFEL structure of oxidised Ribonucleotide reductase R2a Y122F mutant from E. coli
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MXR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 5.5 297 0.1M Bis-Tris pH 5.5, PEG 3350 25%
Crystal Properties Matthews coefficient Solvent content 2.38 48.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.96 α = 90 b = 76.549 β = 90 c = 145.738 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 297 CCD RAYONIX MX340-HS 2024-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE MFX 1.262950 SLAC LCLS MFX
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 injection
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.9 36.43 99.94 0.98 5.831 20 65872 22.41
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 0.41
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.9 36.43 1.33 65872 2003 99.94 0.1519 0.1508 0.1522 0.1853 0.1862 24.9
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.1308 f_angle_d 1.3433 f_chiral_restr 0.0884 f_bond_d 0.0171 f_plane_restr 0.0127
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5576 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement cctbx.xfel data reduction cxi.merge data scaling PHENIX phasing