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X-ray pump X-ray probe on lysozyme.Gd nanocrystals: 37 fs time delay
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N5R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 3 277 20 % NACL, 6 % PEG 6000, 0.1 M SODIUM acetate pH 3.0
Crystal Properties Matthews coefficient Solvent content 1.9 35.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79 α = 90 b = 79 β = 90 c = 39.5 γ = 90
Symmetry Space Group P 43 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 CS-PAD CXI-1 2015-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE CXI 1.75 SLAC LCLS CXI
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 GDVN injection injection
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 15 (fs) 120 0.025 7.07 (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 16000 16000
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 GDVN undefined (µl/min) undefined (µm)
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 2.32 22.81 100 0.981 0.083 12.4 1 5315 28.9
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 2.32 2.36 0.972 0.086 11.7
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4n5r 2.3 22.81 5315 591 99.85 0.2352 0.2289 0.2364 0.2943 0.3007 RANDOM 23.53
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] -0.03 -0.03 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.487 r_dihedral_angle_4_deg 19.833 r_dihedral_angle_3_deg 12.923 r_dihedral_angle_1_deg 7.495 r_angle_refined_deg 1.512 r_angle_other_deg 1.212 r_chiral_restr 0.055 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.487 r_dihedral_angle_4_deg 19.833 r_dihedral_angle_3_deg 12.923 r_dihedral_angle_1_deg 7.495 r_angle_refined_deg 1.512 r_angle_other_deg 1.212 r_chiral_restr 0.055 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 992 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystFEL data reduction XSCALE data scaling REFMAC phasing