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SS-ROX structure analysis of H-Ras using caged-compound complex: 15 min after UV light irradiation (GTP bound form state 1)
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K8Y amino acid models of residue number 29-39, 61-74, and 96-109 are truncated
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6.4 298 18% w/v PEG 8000, 0.2M calcium acetate, 0.1M MES pH 6.4, microseeding
Crystal Properties Matthews coefficient Solvent content 2.58 52.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.362 α = 90 b = 92.362 β = 90 c = 121.18 γ = 120
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 2021-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target fixed target
Fixed Target Diffraction ID Description Sample Holding Support Base Motion control Details Sample Solvent 1 microcrystal suspension was fished by loop microcrystals were holded with frozen cryoprotectant goniometer QKSU0 0.25 degree rotation per frame 15% w/v PEG 8000, 0.166 M calcium acetate, 0.083 M MES pH 6.4, 16.6% v/v PEG 400
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 undefined (fs) undefined (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 20963 32068 20963
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 67.11 100 0.989 0.107 8.37 612.5 13676 21.79
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 2.02 100 0.597 0.6574 1.78 400
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 2 48.3 1.35 13673 689 99.99 0.1857 0.1846 0.1848 0.2069 0.2071 25.96
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 21.5279 f_angle_d 0.7626 f_chiral_restr 0.0474 f_bond_d 0.004 f_plane_restr 0.0038
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1218 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 34
Software Software Software Name Purpose PHENIX refinement CrystFEL data reduction CrystFEL data scaling PHASER phasing