☰ Navigation Tabs
The structure of cyclin-dependent kinase 2 (CDK2) in complex with Compound 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GZ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 12% (w/v) PEG 3350, 0.10 M MES pH=7.00
Crystal Properties Matthews coefficient Solvent content 2.07 40.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.851 α = 90 b = 73.035 β = 90 c = 70.731 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2018-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.999891638756 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.53 50.81 98.6 0.055 14.57 4.1 42212
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.53 1.78 99.4 0.517 3.47 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1GZ8 1.53 50.81 38061 4150 98.63 0.1804 0.1764 0.1879 0.2175 0.2243 RANDOM 24.955
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] -0.02 -0.35 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.053 r_sphericity_free 17.305 r_dihedral_angle_3_deg 13.196 r_dihedral_angle_4_deg 12.592 r_dihedral_angle_1_deg 5.459 r_sphericity_bonded 5.402 r_rigid_bond_restr 3.948 r_angle_other_deg 1.7 r_angle_refined_deg 1.45 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.053 r_sphericity_free 17.305 r_dihedral_angle_3_deg 13.196 r_dihedral_angle_4_deg 12.592 r_dihedral_angle_1_deg 5.459 r_sphericity_bonded 5.402 r_rigid_bond_restr 3.948 r_angle_other_deg 1.7 r_angle_refined_deg 1.45 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2339 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 37
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing