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Crystal structure of a benzthiophene inhibitor bound to human Cyclin-dependent Kinase-2 (CDK-2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AQ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 CDK-1 at 2.5 mg/ml is equilibrated against a well solution containing 14% PEG 4000, 50 mM ammonium acetate, 50 mM Hepes pH 7.5, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.05 40.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.717 α = 90 b = 71.709 β = 90 c = 72.242 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++ 2005-01-07 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
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 1.9 30 99 0.04 29.843 4.2 22384
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) 1.9 1.97 98.9 0.334 3.7 2185
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 1AQ1 1.9 27.66 22346 1147 98.96 0.212 0.21 0.2086 0.259 0.2572 RANDOM 30.062
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] -0.07 0.24 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.287 r_dihedral_angle_4_deg 17.684 r_dihedral_angle_3_deg 14.544 r_dihedral_angle_1_deg 4.998 r_scangle_it 3.15 r_scbond_it 1.923 r_mcangle_it 1.473 r_angle_refined_deg 1.21 r_mcbond_it 0.8 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.287 r_dihedral_angle_4_deg 17.684 r_dihedral_angle_3_deg 14.544 r_dihedral_angle_1_deg 4.998 r_scangle_it 3.15 r_scbond_it 1.923 r_mcangle_it 1.473 r_angle_refined_deg 1.21 r_mcbond_it 0.8 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2284 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 19
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction AMoRE phasing