1R8J

Crystal Structure of Circadian Clock Protein KaiA from Synechococcus elongatus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1M2EPDB ENTRY 1M2E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION6.5298Ammonium Sulfate, Sodium Cacodylate, PEG 8000, Glycerol, pH 6.5, EVAPORATION, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.346.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.111α = 90
b = 125.818β = 114.9
c = 56.818γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9792APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
125095.20.040.0430.63.638494
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.0754.30.3620.3622.7

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 DIFFRACTIONcombination of SAD phasing, real space molecular replacement, ARP/wARP phase improvement, and non-crystallographic symmetry averagingTHROUGHOUTPDB ENTRY 1M2E2.032036552190598.920.213060.210120.27144RANDOM39.112
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]
-0.391.54-0.362.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.389
r_scangle_it2.928
r_scbond_it1.745
r_mcangle_it1.436
r_angle_refined_deg1.116
r_mcbond_it0.756
r_symmetry_vdw_refined0.297
r_nbd_refined0.192
r_symmetry_hbond_refined0.162
r_xyhbond_nbd_refined0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.389
r_scangle_it2.928
r_scbond_it1.745
r_mcangle_it1.436
r_angle_refined_deg1.116
r_mcbond_it0.756
r_symmetry_vdw_refined0.297
r_nbd_refined0.192
r_symmetry_hbond_refined0.162
r_xyhbond_nbd_refined0.13
r_chiral_restr0.083
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4331
Nucleic Acid Atoms
Solvent Atoms246
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing