X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5FQD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8277.15CSNK1A1 at a concentration of 5.8 mg/ml (50 mM Tris-HCl, 300 mM NaCl, 0.25 mM TCEP, pH 8.0) was pre-incubated with 0.7 mM (4.7-fold molar excess) of Mg2+-ATP (120 mM in UPW) for 1 h. 0.1 uL of the protein solution was then mixed with 0.1 uL of reservoir solution (0.10 M MES/NaOH pH 6.8, 10.0% 2-propanol, 26.0% PEG400) and equilibrated at 4 C over 0.06mL of reservoir solution. Well diffracting crystals appeared within 4 days and grew to full size over 23 days.
Crystal Properties
Matthews coefficientSolvent content
3.0259.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.383α = 90
b = 113.383β = 90
c = 80.878γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100.5PIXELDECTRIS PILATUS3 2M2017-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.966ESRFMASSIF-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
12.2829.3198.10.0713.3422991
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.282.40.56

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 REPLACEMENTTHROUGHOUT5FQD2.2829.3121917107198.010.177090.174960.22117RANDOM58.303
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]
-0.21-0.210.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.433
r_dihedral_angle_3_deg13.346
r_dihedral_angle_4_deg11.595
r_long_range_B_refined9.954
r_long_range_B_other9.949
r_scangle_other7.515
r_mcangle_it6.226
r_mcangle_other6.224
r_dihedral_angle_1_deg5.586
r_scbond_it5.056
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.433
r_dihedral_angle_3_deg13.346
r_dihedral_angle_4_deg11.595
r_long_range_B_refined9.954
r_long_range_B_other9.949
r_scangle_other7.515
r_mcangle_it6.226
r_mcangle_other6.224
r_dihedral_angle_1_deg5.586
r_scbond_it5.056
r_scbond_other5.055
r_mcbond_it4.327
r_mcbond_other4.325
r_angle_other_deg3.585
r_angle_refined_deg1.182
r_chiral_restr0.075
r_bond_refined_d0.008
r_gen_planes_other0.006
r_gen_planes_refined0.004
r_bond_other_d
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 Atoms2456
Nucleic Acid Atoms
Solvent Atoms190
Heterogen Atoms141

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
REFMACphasing
MOSFLMdata reduction