9CGG | pdb_00009cgg

Human DJ-1, 30 sec mixing with methylglyoxal, pink beam time-resolved serial crystallography, CrystFEL processed


X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherUnpublished DJ-1 structure from X-ray source

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE7.5293100 mM HEPES, 200 mM NaCl, 15% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.1560.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.03α = 90
b = 76.03β = 90
c = 76.14γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDRAYONIX MX340-HS2022-11-12LLAUE
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-ID-B1.240-1.016APS14-ID-B

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1concentric flow microfluidic mixerinjection
Data Reduction
Diffraction IDFrames IndexedCrystal HitsFrames IndexedLatices Merged
1100710511007

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
11.7765.8498.980.980.13753.6460.652499327.93
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)
11.771.898.70.0458.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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)Mean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISFREE R-VALUE2.0132.961.341719686199.050.16310.1620.16160.18210.18134.18
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.063
f_angle_d0.5099
f_chiral_restr0.0434
f_plane_restr0.0031
f_bond_d0.0019
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1383
Nucleic Acid Atoms
Solvent Atoms113
Heterogen Atoms5

Software

Software
Software NamePurpose
PHENIXrefinement
Precognitiondata reduction
CrystFELdata scaling
PHENIXphasing