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Structure of Ribonucleotide reductase R2 from Escherichia coli collected by femtosecond serial crystallography on a COC membrane
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 VAPOR DIFFUSION, SITTING DROP 7 294 34-37 % PAA 2100, 100 mM HEPES 7.0, 250-450 mM NaCl, 200 mM ammonium sulfate
[and]
26% PAA 2100, 100 mM HEPES 7.0, 150 NaCl, 100 Malonate
Crystal Properties Matthews coefficient Solvent content 2.88 57.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.6 α = 90 b = 91.6 β = 90 c = 207.2 γ = 120
Symmetry Space Group P 61 2 2
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 PSI JUNGFRAU 16M 2019-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SwissFEL ARAMIS BEAMLINE ESB 1.359 SwissFEL ARAMIS ESB
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
Fixed Target Diffraction ID Description Sample Holding Support Base Motion control Details Sample Solvent 1 SwissMX CM COC membrane SwissMX goniometer
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 undefined (fs) 9.12 (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 7500 7500
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) R Split (All) 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 2.29 19.91 100 0.9936 0.0863 6.65 175 23626 59.66
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.29 2.33 0.3532 1.069 1.27
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1MXR 2.3 19.91 1.34 23621 1182 99.97 0.2074 0.2054 0.2056 0.2451 0.246 83.39
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 16.1696 f_angle_d 0.5103 f_chiral_restr 0.0382 f_plane_restr 0.0031 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2781 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 2
Software Software Software Name Purpose CrystFEL data reduction CrystFEL data scaling PHENIX refinement PHASER phasing Coot model building