6SR5

X-ray pump X-ray probe on lysozyme.Gd nanocrystals: 102 fs time delay


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4N5R 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE327720 % NACL, 6 % PEG 6000, 0.1 M SODIUM acetate pH 3.0
Crystal Properties
Matthews coefficientSolvent content
1.935.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79α = 90
b = 79β = 90
c = 39.5γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELCS-PAD CXI-12015-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE CXI1.75SLAC LCLSCXI

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1GDVN injectioninjection
Measurement
Diffraction IDPulse DurationPulse Repetition RateFocal Spot SizePulse EnergyPhotons Per Pulse
1151200.0257.07

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)R Split (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.3222.811000.9770.1078.515315
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.323.360.9510.137.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4n5r2.322.81531559199.850.19060.18510.2415RANDOM29.795
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.058
r_dihedral_angle_4_deg21.375
r_dihedral_angle_3_deg13.119
r_dihedral_angle_1_deg7.278
r_angle_refined_deg1.786
r_angle_other_deg1.234
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.058
r_dihedral_angle_4_deg21.375
r_dihedral_angle_3_deg13.119
r_dihedral_angle_1_deg7.278
r_angle_refined_deg1.786
r_angle_other_deg1.234
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms992
Nucleic Acid Atoms
Solvent Atoms26
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CrystFELdata reduction
XSCALEdata scaling
REFMACphasing