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
1.9737.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.321α = 90
b = 71.296β = 90
c = 72.114γ = 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
11.550.751000.0513.56.944735
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.531001.57.1

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 REPLACEMENTTHROUGHOUT5MHQ1.550.7542508222799.970.201190.198930.2433RANDOM33.24
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]
0.180.9-1.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.864
r_dihedral_angle_4_deg17.807
r_dihedral_angle_3_deg15.817
r_long_range_B_refined8.023
r_long_range_B_other8.023
r_scangle_other6.116
r_dihedral_angle_1_deg6.08
r_mcangle_other4.321
r_mcangle_it4.318
r_scbond_it4.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.864
r_dihedral_angle_4_deg17.807
r_dihedral_angle_3_deg15.817
r_long_range_B_refined8.023
r_long_range_B_other8.023
r_scangle_other6.116
r_dihedral_angle_1_deg6.08
r_mcangle_other4.321
r_mcangle_it4.318
r_scbond_it4.095
r_scbond_other4.095
r_angle_other_deg3.573
r_mcbond_it3.222
r_mcbond_other3.213
r_angle_refined_deg2.092
r_chiral_restr0.138
r_bond_refined_d0.021
r_gen_planes_other0.018
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 Atoms2302
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing