3PXF

CDK2 in complex with two molecules of 8-anilino-1-naphthalene sulfonate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PW2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52915 mg/mL CDK2, 5 mM ANS, 15% (v/v) JEFFAMINE ED-2001, 50 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.9336.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.01α = 90
b = 69.45β = 90
c = 72.29γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93IMAGE PLATERIGAKUmirrors2010-06-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54178

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
11.82098.50.199213.32499824998-317.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8596.60.0353.81.91872

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1PW21.819.52499824998110098.40.1980.1980.229RANDOM25.8
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]
-3.324.19-0.87
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.7
c_scangle_it2.64
c_mcangle_it2.18
c_scbond_it1.75
c_angle_deg1.4
c_mcbond_it1.31
c_improper_angle_d0.84
c_bond_d0.01
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.7
c_scangle_it2.64
c_mcangle_it2.18
c_scbond_it1.75
c_angle_deg1.4
c_mcbond_it1.31
c_improper_angle_d0.84
c_bond_d0.01
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2431
Nucleic Acid Atoms
Solvent Atoms192
Heterogen Atoms62

Software

Software
Software NamePurpose
StructureStudiodata collection
CNSrefinement
XDSdata reduction
XDSdata scaling
CNSphasing