8A9E

Lysozyme, 9-11 fs FEL pulses as determined by XTCAV


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE429310 % NaCl, 0.1 M sodium acetate buffer, pH 4.0, soaked in 100 mM gadoteridol 30 min. before data collection
Crystal Properties
Matthews coefficientSolvent content
2.0540.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.75α = 90
b = 77.75β = 90
c = 38.9γ = 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 CXI1.393SLAC LCLSCXI

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1injection

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
11.6422.451000.9230.2373.4115159
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)
11.641.681000.4110.831.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISFREE R-VALUE4N5R1.66522.4515119151299.6970.2050.20110.239618.706
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]
-0.003-0.0030.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.826
r_dihedral_angle_4_deg21.87
r_dihedral_angle_3_deg14.639
r_dihedral_angle_1_deg6.938
r_lrange_it4.65
r_lrange_other4.625
r_scangle_it3.723
r_scangle_other3.721
r_scbond_it2.478
r_scbond_other2.476
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.826
r_dihedral_angle_4_deg21.87
r_dihedral_angle_3_deg14.639
r_dihedral_angle_1_deg6.938
r_lrange_it4.65
r_lrange_other4.625
r_scangle_it3.723
r_scangle_other3.721
r_scbond_it2.478
r_scbond_other2.476
r_mcangle_other1.89
r_mcangle_it1.888
r_angle_refined_deg1.57
r_angle_other_deg1.45
r_mcbond_it1.352
r_mcbond_other1.288
r_nbd_refined0.223
r_symmetry_nbd_other0.2
r_nbd_other0.191
r_xyhbond_nbd_refined0.184
r_nbtor_refined0.168
r_symmetry_xyhbond_nbd_refined0.133
r_symmetry_nbtor_other0.092
r_chiral_restr0.09
r_symmetry_nbd_refined0.077
r_metal_ion_refined0.051
r_bond_refined_d0.009
r_gen_planes_refined0.008
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 Atoms52
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
REFMACphasing