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Crystal structure of human CDK2 complexed with a thiazolidinone inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B39 PDB ENTRY 1B39
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 VAPOR DIFFUSION HANGING DROP, ROOM TEMPERATURE, PEG3350, HEPES PH7.2, AMMONIUM ACETATE, pH 7.00
Crystal Properties Matthews coefficient Solvent content 2 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.591 α = 90 b = 71.454 β = 90 c = 72.284 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 IMAGE PLATE RIGAKU (MSC) MIRRORS 2003-12-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.1 30 99.5 0.17 6.2 4.4 16796 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.17 96 0.5 2.7 4.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1B39 2.3 15 11829 906 99.6 0.206 0.199 0.297 0.2681 RANDOM 28.9
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] -0.19 1.54 -1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.483 r_dihedral_angle_3_deg 19.729 r_dihedral_angle_4_deg 14.51 r_dihedral_angle_1_deg 6.916 r_scangle_it 3.45 r_scbond_it 2.273 r_angle_refined_deg 1.863 r_mcangle_it 1.542 r_mcbond_it 0.907 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.483 r_dihedral_angle_3_deg 19.729 r_dihedral_angle_4_deg 14.51 r_dihedral_angle_1_deg 6.916 r_scangle_it 3.45 r_scbond_it 2.273 r_angle_refined_deg 1.863 r_mcangle_it 1.542 r_mcbond_it 0.907 r_nbtor_refined 0.32 r_symmetry_vdw_refined 0.299 r_nbd_refined 0.246 r_symmetry_hbond_refined 0.215 r_xyhbond_nbd_refined 0.186 r_chiral_restr 0.119 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2240 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction d*TREK data scaling MOLREP phasing