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Crystal structure of ribonucleotide reductase R2 subunit solved by serial synchrotron crystallography
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Unpublished
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 4.5 294 16% (w/v) polyethylene glycol 3350, 2% (v/v) tacsimate pH 4.5
Crystal Properties Matthews coefficient Solvent content 2 38.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.32 α = 90 b = 64.32 β = 90 c = 153.15 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL DECTRIS EIGER X 16M 2019-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.98 MAX IV BioMAX
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 Silicon nitride membranes fixed target
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 2.4 59.3 98.6 0.99 6.73 516 13245 81.8
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 2.4 2.58 0.64
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R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE Unpublished 2.4 59.3 13060 653 98.6 0.1757 0.1734 0.1825 0.221 0.2279 90.39
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 23.4779 f_angle_d 0.4918 f_chiral_restr 0.0354 f_plane_restr 0.0029 f_bond_d 0.0028
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2493 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement MxCuBE data collection PHENIX phasing CrystFEL data scaling Coot model building CrystFEL data reduction