5OO3

Cdk2(F80C, C177A) with covalent ligand at F80C


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2989 - 15% w/v, 50 mM HEPES, 50 mM sodium/potassium phosphate
Crystal Properties
Matthews coefficientSolvent content
1.9938.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.11α = 90
b = 70.97β = 90
c = 72.43γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152017-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.7336.6799.710.08530.999313.827.1929150
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.731.7699.861.65850.56091.077.4

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 REPLACEMENTTHROUGHOUT4EK31.7336.6727745140499.70.187290.18430.2491RANDOM33.251
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]
3.03-2.28-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.894
r_dihedral_angle_4_deg20.651
r_dihedral_angle_3_deg14.662
r_long_range_B_refined9.01
r_dihedral_angle_1_deg5.536
r_scbond_it4.281
r_mcangle_it4.117
r_mcbond_it2.996
r_angle_refined_deg1.891
r_chiral_restr0.129
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.894
r_dihedral_angle_4_deg20.651
r_dihedral_angle_3_deg14.662
r_long_range_B_refined9.01
r_dihedral_angle_1_deg5.536
r_scbond_it4.281
r_mcangle_it4.117
r_mcbond_it2.996
r_angle_refined_deg1.891
r_chiral_restr0.129
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2284
Nucleic Acid Atoms
Solvent Atoms276
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing