6GVA

CDK2/cyclin A2 in complex with pyrazolo[4,3-d]pyrimidine inhibitor LGR4455


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529110% w/v PEG 20000, 20% v/v PEG MME 550, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.03 M sodium iodide, and 0.1 M bicine/Trizma base, pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.5752

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.015α = 90
b = 112.642β = 90
c = 159.69γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MSagitally bended Si111-crystal2018-01-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.154898.30.1950.2120.9947.966.2473477338.407
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.2890.31.4561.6640.2980.864.295

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 REPLACEMENTTHROUGHOUT5LMK2.154833033173998.310.19660.19430.2403RANDOM39.552
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]
-0.03-0.060.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.098
r_dihedral_angle_4_deg16.021
r_dihedral_angle_3_deg15.444
r_dihedral_angle_1_deg6.104
r_angle_refined_deg1.619
r_angle_other_deg1.02
r_chiral_restr0.092
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.098
r_dihedral_angle_4_deg16.021
r_dihedral_angle_3_deg15.444
r_dihedral_angle_1_deg6.104
r_angle_refined_deg1.619
r_angle_other_deg1.02
r_chiral_restr0.092
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4402
Nucleic Acid Atoms
Solvent Atoms160
Heterogen Atoms73

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing