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Crystal structure of human CDK2 complexed with a pyrazolo[1,5-a]pyrimidine 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 7.2 293 Peg 3350, Hepes, Ammonium acetate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2 37.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.372 α = 90 b = 71.423 β = 90 c = 72.004 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 RAXIS IV++ mirrors 2003-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
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 1.8 30 92.9 0.085 7.8 2.65 24371 24371 1 1 18.4
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) 1.8 1.86 64.2 0.38 2.2 1.92 2575
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 pdb entry 1B39 2.15 25 1 14741 14431 752 97.9 0.2009 0.19612 0.1997 0.29511 0.295 RANDOM 39.164
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] 0.01 0.64 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.492 r_scangle_it 4.409 r_scbond_it 2.964 r_angle_refined_deg 2.076 r_mcangle_it 1.941 r_mcbond_it 1.099 r_nbd_refined 0.266 r_symmetry_vdw_refined 0.246 r_symmetry_hbond_refined 0.222 r_xyhbond_nbd_refined 0.203
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.492 r_scangle_it 4.409 r_scbond_it 2.964 r_angle_refined_deg 2.076 r_mcangle_it 1.941 r_mcbond_it 1.099 r_nbd_refined 0.266 r_symmetry_vdw_refined 0.246 r_symmetry_hbond_refined 0.222 r_xyhbond_nbd_refined 0.203 r_chiral_restr 0.146 r_bond_refined_d 0.022 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2282 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction d*TREK data scaling MOLREP phasing