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SS-ROX structure analysis of H-Ras using caged-compound complex: freeze-trap series (10 hr after UV light irradiation)
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 2.59 52.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.515 α = 90 b = 92.515 β = 90 c = 121.521 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 EIGER2 XE 16M 2025-02-13 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 41331 73916 41331
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 1.8 66.89 100 0.9954 0.0887 10.63 1027.6 18777 17.26
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 1.8 1.83 100 0.5439 0.7281 827.3
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 1.8 66.89 1.35 18774 942 99.98 0.1859 0.1841 0.185 0.2189 0.2198 23.55
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 23.2418 f_angle_d 1.3567 f_chiral_restr 0.0777 f_bond_d 0.0148 f_plane_restr 0.0115
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1224 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 62
Software Software Software Name Purpose PHENIX refinement CrystFEL data reduction CrystFEL data scaling PHASER phasing