8C9J | pdb_00008c9j

Crystal structure of human NQO1 by serial femtosecond crystallography


X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DXQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE8.52930.1 M Tris pH 8.5, 0.2 M sodium acetate, 20% polyethylene glycol (PEG) 3350, 20 um FAD
Crystal Properties
Matthews coefficientSolvent content
2.6553.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.4α = 90
b = 107.6β = 90
c = 198.1γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELSLAC ePix10k2021-05-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE MFX1.2848SLAC LCLSMFX

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1Modular Droplet Injectorinjection
Data Reduction
Diffraction IDFrames IndexedCrystal HitsFrames IndexedLatices Merged
1
Injection
Diffraction IDDescriptionFlow RateInjector DiameterInjection PowerInjector NozzleFilter SizeCarrier Solvent
1Modular Droplet Injector5 (µl/min)undefined (µm)Crystals in mother liquor encapsulated into oil droplets

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.7241000.96681.94636928
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.81000.458

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1DXQ2.723.92236835182299.7240.2270.2250.230.26870.270.145.992
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]
0.3630.054-0.417
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.632
r_dihedral_angle_6_deg14.859
r_dihedral_angle_2_deg8.131
r_lrange_it7.232
r_lrange_other7.232
r_dihedral_angle_1_deg6.698
r_scangle_it4.699
r_scangle_other4.699
r_mcangle_it4.172
r_mcangle_other4.172
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8646
Nucleic Acid Atoms
Solvent Atoms163
Heterogen Atoms228

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
Aimlessdata scaling
PHASERphasing