1U3C

Crystal Structure of the PHR domain of Cryptochrome 1 from Arabidopsis thaliana


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DNPE.coli DNA photolyase, pdb entry 1DNP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5309glycerol, MES, sulfobetaine-195, 1,6-hexanediol, sodium, potassium tartrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 309K
Crystal Properties
Matthews coefficientSolvent content
3.767

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 169.43α = 90
b = 169.43β = 90
c = 104.245γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDCUSTOM-MADE2004-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.979APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.65096.50.09426.512.42645226452-347.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.62.6997.60.8062.89.92627

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTE.coli DNA photolyase, pdb entry 1DNP2.634.62508325083247790.90.210.2050.2050.254RANDOM47.9
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]
8.7911.918.79-17.58
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.5
c_scangle_it7.67
c_scbond_it5.82
c_mcangle_it4.91
c_mcbond_it3.41
c_angle_deg1.5
c_improper_angle_d0.96
c_bond_d0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3941
Nucleic Acid Atoms
Solvent Atoms68
Heterogen Atoms85

Software

Software
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing