7UP4

Crystal structure of C-terminal Domain of MSK1 in complex with covalently bound pyrrolopyrimidine compound 20 (co-crystal)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherin-house model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5289Crystals were produced by sitting drop vapor diffusion with an equal volume of the protein, Msk1-C terminal domain (PID7059-1, CID101276) at 7.6 mg/ml in 25mM HEPES pH 7.5, 150mM NaCl, 5% Glycerol, 5mM BME and a crystallization buffer containing 20mM of each DL-glutamic acid, DL-alanine, glycine, DL-lysine, DL-serine, sodium HEPES / MOPS (acid) pH 7.5, 12.5% (V/V) MPD, 12.5% (w/V) PEG 1000, 12.5% (w/V) PEG 3350 (tray ID 320260, well H8, Molecular Dimensions / Calibre Morpheus screen ). Crystals were direly vitrified in in liquid N2. Puck ID CNL6-3
Crystal Properties
Matthews coefficientSolvent content
2.3146.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.44α = 90
b = 91.18β = 90
c = 136.17γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002021-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
135099.70.1090.1260.99411.273.9991338043.356
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.081000.5750.6630.7812.464.094

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEin-house model348.121.3513376127399.710.19840.19060.2707054.11
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.5726
f_angle_d0.629
f_chiral_restr0.0418
f_bond_d0.0042
f_plane_restr0.0041
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4466
Nucleic Acid Atoms
Solvent Atoms5
Heterogen Atoms32

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing