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SS-ROX structure analysis of H-Ras using caged-compound complex: 28 hr after UV light irradiation (GDP bound form)
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 2.68 54.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.436 α = 90 b = 93.436 β = 90 c = 122.847 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 298 PIXEL DECTRIS EIGER X 16M 2018-11-13 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 coated with polyvinyl alcohol microcrystals were holded in controlled humid air goniometer QKSU0 0.25 degree rotation per frame 18% PEG8000, 0.2 M calcium acetate, 0.1 M MES pH 6.4
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 undefined (fs) undefined (KeV)
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 2.5 67.61 100 0.9736 0.2636 3.99 111.9 7351 27.82
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 2.5 2.54 100 0.3639 1.1398 1.04 74.5
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.5 67.58 1.34 7298 347 99.28 0.1988 0.1973 0.1973 0.2281 0.2282 Random selection 31.16
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] 0.010703 0.006179 0.012358 0.00814
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.5438 f_angle_d 0.4699 f_chiral_restr 0.0429 f_plane_restr 0.0028 f_bond_d 0.0015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1195 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 33
Software Software Software Name Purpose PHENIX refinement CrystFEL data reduction CrystFEL data scaling PHASER phasing