6Y2N

Crystal structure of ribonucleotide reductase R2 subunit solved by serial synchrotron crystallography


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherUnpublished

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE4.529416% (w/v) polyethylene glycol 3350, 2% (v/v) tacsimate pH 4.5
Crystal Properties
Matthews coefficientSolvent content
238.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.32α = 90
b = 64.32β = 90
c = 153.15γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS EIGER X 16M2019-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX0.98MAX IVBioMAX

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1Silicon nitride membranesfixed target

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
12.459.398.60.996.735161324581.8
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)
12.42.580.64

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-FreeMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISFREE R-VALUEUnpublished2.459.31306065398.60.17570.17340.22190.39
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_d23.4779
f_angle_d0.4918
f_chiral_restr0.0354
f_plane_restr0.0029
f_bond_d0.0028
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2493
Nucleic Acid Atoms
Solvent Atoms23
Heterogen Atoms2

Software

Software
Software NamePurpose
PHENIXrefinement
MxCuBEdata collection
PHENIXphasing
CrystFELdata scaling
Cootmodel building
CrystFELdata reduction