3DVL

Crystal Structure of Full Length Circadian Clock Protein KaiC with Correct Geometry at Phosphorylation Sites


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4291SODIUM FORMATE, GLYCEROL, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.6453.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 132.873α = 90
b = 135.576β = 90
c = 204.951γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray103CCDMARRESEARCH2003-06-01MMAD
21x-rayCCDMARRESEARCH2002-07-10MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.25APS22-ID
2SYNCHROTRONAPS BEAMLINE 5ID-B1APS5ID-B

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
1,22.83099.60.04320.698775087750
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)
2.82.999.30.5012.2

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONrefinementTHROUGHOUTPDB entry 2GBL2.8307974675705404189.60.23920.288random73.676
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]
-12.208-3.33915.548
RMS Deviations
KeyRefinement Restraint Deviation
c_angle_d2.1166
c_bond_d0.021694
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms23426
Nucleic Acid Atoms
Solvent Atoms66
Heterogen Atoms378

Software

Software
Software NamePurpose
RAVEmodel building
GLRFphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RAVEphasing