5ZM0

X-ray structure of animal-like Cryptochrome from Chlamydomonas reinhardtii


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3CVV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
4VAPOR DIFFUSION, HANGING DROP291.1 M 2-(N-morpholino)ethanesulfonic acid (MES), pH 6.0, 35 % PEG 4000

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.21α = 90
b = 65.12β = 90
c = 151.98γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252013-12-19MSINGLE WAVELENGTH
22x-ray100CCDRAYONIX MX300-HS2018-03-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.30.8944BESSY14.3
2SYNCHROTRONNSRRC BEAMLINE TPS 05A0.999840NSRRCTPS 05A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.639.761000.2750.2860.9928.513.296664510.01
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6571001.681.7770.5061.310.16

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3CVV1.639.766662133021000.15260.1881random selection15.17
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]
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3874
Nucleic Acid Atoms
Solvent Atoms774
Heterogen Atoms113

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing