7DYK

Crystal Structure of Cyanobacterial Circadian Clock Protein KaiC


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7DYJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION7313sodium/pottasium tartrae, sodium acetate, KCl

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.847α = 90
b = 94.847β = 90
c = 180.56γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

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
12.9948.5599.70.13812.910.419313
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)
133.110.962

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT7DYJ2.9948.551752388199.720.27640.27380.3279RANDOM62.867
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]
-4.92-2.46-4.9215.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.234
r_dihedral_angle_3_deg22.815
r_dihedral_angle_4_deg20.207
r_dihedral_angle_1_deg3.313
r_angle_refined_deg1.223
r_angle_other_deg1.111
r_chiral_restr0.027
r_bond_refined_d0.002
r_gen_planes_refined0.002
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.234
r_dihedral_angle_3_deg22.815
r_dihedral_angle_4_deg20.207
r_dihedral_angle_1_deg3.313
r_angle_refined_deg1.223
r_angle_other_deg1.111
r_chiral_restr0.027
r_bond_refined_d0.002
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6564
Nucleic Acid Atoms
Solvent Atoms13
Heterogen Atoms128

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing