5YZ8

Crystal Structure of N-terminal C1 domain of KaiC


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4TL7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293PEG 400, PEG 8000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties
Matthews coefficientSolvent content
2.244.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.072α = 90
b = 108.072β = 90
c = 224.069γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2016-07-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU1.0SPring-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
12.8501000.08620.310.837912
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.91002.410.8

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4TL72.815035801190099.50.2440.2410.339.12
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]
-0.11-0.06-0.110.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.988
r_dihedral_angle_4_deg17.433
r_dihedral_angle_3_deg16.308
r_dihedral_angle_1_deg7.467
r_long_range_B_refined3.706
r_long_range_B_other3.704
r_mcangle_it2.102
r_mcangle_other2.102
r_scangle_other1.772
r_angle_refined_deg1.255
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.988
r_dihedral_angle_4_deg17.433
r_dihedral_angle_3_deg16.308
r_dihedral_angle_1_deg7.467
r_long_range_B_refined3.706
r_long_range_B_other3.704
r_mcangle_it2.102
r_mcangle_other2.102
r_scangle_other1.772
r_angle_refined_deg1.255
r_mcbond_it1.212
r_mcbond_other1.212
r_scbond_it1.013
r_scbond_other1.013
r_angle_other_deg0.914
r_chiral_restr0.06
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.003
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9640
Nucleic Acid Atoms
Solvent Atoms37
Heterogen Atoms198

Software

Software
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
REFMACrefinement