X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HCKHuman CDK2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.4277Na Citrate, Na Acetate, PEG 4000, glycerol, NDSB201, ATP, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 4.0K
Crystal Properties
Matthews coefficientSolvent content
3.6365.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.501α = 90
b = 191.635β = 94.4
c = 75.794γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42003-11-22MSINGLE WAVELENGTH
21100CCDMARRESEARCHMicrofocus beamline ID13 at ESRF2003-12-06
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.9756ESRFID29
2SYNCHROTRONESRF BEAMLINE ID130.9789ESRFID13

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.9649.4592.90.1290.1299.53.83812235416173.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.023.1870.10.4660.4661.61.73851

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTHuman CDK23.0249.453327133271175795.480.216590.216590.212740.2879RANDOM44.013
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]
4.22-0.05-2.56-1.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.62
r_dihedral_angle_3_deg24.144
r_dihedral_angle_4_deg19.748
r_dihedral_angle_1_deg8.773
r_scangle_it2.453
r_angle_refined_deg1.923
r_scbond_it1.463
r_mcangle_it1.277
r_mcbond_it0.698
r_symmetry_hbond_refined0.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.62
r_dihedral_angle_3_deg24.144
r_dihedral_angle_4_deg19.748
r_dihedral_angle_1_deg8.773
r_scangle_it2.453
r_angle_refined_deg1.923
r_scbond_it1.463
r_mcangle_it1.277
r_mcbond_it0.698
r_symmetry_hbond_refined0.35
r_nbtor_refined0.335
r_symmetry_vdw_refined0.312
r_nbd_refined0.284
r_xyhbond_nbd_refined0.225
r_chiral_restr0.136
r_bond_refined_d0.016
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9164
Nucleic Acid Atoms
Solvent Atoms48
Heterogen Atoms124

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
CCP4data scaling