X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29310MG/ML CDK2 10% V/V PEG3350, 50 MM HEPES/NAOH, 50 MM NA/K PHOSPHATE, PH 7.5
Crystal Properties
Matthews coefficientSolvent content
238.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.291α = 90
b = 71.938β = 90
c = 72.391γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.987DiamondI04

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
11.351.081000.0415.56.969081
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.321001.36.8

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5MHQ1.351.0865481360099.950.205690.204150.23204RANDOM28.149
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]
-0.38-1.21.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.427
r_dihedral_angle_4_deg25.073
r_dihedral_angle_3_deg16.733
r_long_range_B_refined8.201
r_long_range_B_other8.165
r_scangle_other6.311
r_dihedral_angle_1_deg5.489
r_scbond_it4.233
r_scbond_other4.233
r_mcangle_it4.041
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.427
r_dihedral_angle_4_deg25.073
r_dihedral_angle_3_deg16.733
r_long_range_B_refined8.201
r_long_range_B_other8.165
r_scangle_other6.311
r_dihedral_angle_1_deg5.489
r_scbond_it4.233
r_scbond_other4.233
r_mcangle_it4.041
r_mcangle_other4.04
r_angle_other_deg3.57
r_mcbond_it2.843
r_mcbond_other2.842
r_angle_refined_deg2.178
r_chiral_restr0.146
r_bond_refined_d0.023
r_gen_planes_other0.019
r_gen_planes_refined0.012
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 Atoms2242
Nucleic Acid Atoms
Solvent Atoms211
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing