☰ Navigation Tabs
HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR 2-Amino-6-(3'-methyl-2'-oxo)butoxypurine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E1V PDB ENTRY 1E1V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.4 PROTEIN AT 10MG/ML IN 15MM NACL, 10MM HEPES, PH7.4, MIXED WITH WELL BUFFER (50MM AMMONIUM ACETATE, 10% PEG4K, 0.1M HEPES PH 7.4) IN EQUAL VOLUMES, THEN VAPOUR DIFFUSION AGAINST WELL BUFFER. CDK2 CRYSTALS WERE SOAKED FOR 20 HOURS IN A SOLUTION OF 0.5MM NU2058 IN 1X WELL BUFFER PREPARED FROM STOCKS 2X WELLBUFFER AND 10MM NU2058 IN 100% DMSO.
Crystal Properties Matthews coefficient Solvent content 1.98 37.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.86 α = 90 b = 71.07 β = 90 c = 71.84 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 CCD MARRESEARCH TORROIDAL MIRROR 1998-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 1.3 20 96.3 0.046 20.2 2.3 63538
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 1.3 1.36 97.2 0.471 1.8 2.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1E1V 1.3 50.64 60158 3380 94.5 0.153 0.151 0.1628 0.185 0.1972 RANDOM 17.44
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] -0.34 1.33 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.761 r_dihedral_angle_1_deg 5.138 r_scangle_it 4.683 r_scbond_it 3.276 r_mcangle_it 2.871 r_angle_other_deg 1.941 r_mcbond_it 1.935 r_angle_refined_deg 1.91 r_symmetry_hbond_other 0.302 r_symmetry_vdw_other 0.284
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.761 r_dihedral_angle_1_deg 5.138 r_scangle_it 4.683 r_scbond_it 3.276 r_mcangle_it 2.871 r_angle_other_deg 1.941 r_mcbond_it 1.935 r_angle_refined_deg 1.91 r_symmetry_hbond_other 0.302 r_symmetry_vdw_other 0.284 r_nbd_refined 0.262 r_xyhbond_nbd_refined 0.242 r_nbd_other 0.218 r_symmetry_hbond_refined 0.204 r_symmetry_vdw_refined 0.174 r_chiral_restr 0.161 r_nbtor_other 0.155 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_xyhbond_nbd_other 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_metal_ion_refined r_metal_ion_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 2342 Nucleic Acid Atoms Solvent Atoms 345 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CCP4 phasing