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Crystal structure of the human CDK2 complexed with the triazolopyrimidine 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 PEG3350, HEPES PH7.2, AMMONIUM ACETATE, VAPOR DIFFUSION HANGING DROP, ROOM TEMPERATURE, pH 7.20
Crystal Properties Matthews coefficient Solvent content 2.09 40.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.578 α = 90 b = 71.611 β = 90 c = 72.296 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 IMAGE PLATE MIRRORS 2003-04-14 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 1.8 30 98.5 0.11 3.7 5.2 26292
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 1.8 1.86 84.1 0.48 1.1 1.96
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 PDB ENTRY 1B39 2.1 15 15325 1419 100 0.21 0.203 0.2135 0.28 0.2894 RANDOM 54.89
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] 1.93 -2.57 0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.433 r_scangle_it 3.735 r_scbond_it 2.366 r_angle_refined_deg 1.569 r_mcangle_it 1.491 r_mcbond_it 0.841 r_nbd_refined 0.225 r_symmetry_vdw_refined 0.21 r_symmetry_hbond_refined 0.199 r_xyhbond_nbd_refined 0.152
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.433 r_scangle_it 3.735 r_scbond_it 2.366 r_angle_refined_deg 1.569 r_mcangle_it 1.491 r_mcbond_it 0.841 r_nbd_refined 0.225 r_symmetry_vdw_refined 0.21 r_symmetry_hbond_refined 0.199 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.099 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined 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 2345 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction d*TREK data scaling MOLREP phasing