7DYE

Crystal Structure of Cyanobacterial Circadian Clock Protein KaiC


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GBL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION7313sodium/potassium tartrate, sodium acetate, KCl
Crystal Properties
Matthews coefficientSolvent content
2.0740.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.906α = 90
b = 94.906β = 90
c = 276.523γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-04-09MSINGLE 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
12.647.599.90.06912.55.328555
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)
12.62.720.612

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 REPLACEMENTTHROUGHOUT2GBL2.647.527082146599.840.28190.27910.3366RANDOM47.208
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]
-6.27-3.13-6.2720.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.438
r_dihedral_angle_3_deg24.243
r_dihedral_angle_4_deg23.898
r_dihedral_angle_1_deg3.537
r_angle_other_deg2.561
r_angle_refined_deg1.249
r_bond_other_d0.039
r_chiral_restr0.03
r_gen_planes_other0.004
r_bond_refined_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.438
r_dihedral_angle_3_deg24.243
r_dihedral_angle_4_deg23.898
r_dihedral_angle_1_deg3.537
r_angle_other_deg2.561
r_angle_refined_deg1.249
r_bond_other_d0.039
r_chiral_restr0.03
r_gen_planes_other0.004
r_bond_refined_d0.003
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6404
Nucleic Acid Atoms
Solvent Atoms22
Heterogen Atoms128

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing