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The structural basis of CDK2 activation by cyclin E
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JST PDB ENTRY 1JST
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 PCDK2/CYCLIN E (6-8 MG/ML), 1 MM AMPPNP, 10-15% PEG3350, 0.2 M SODIUM CITRATE PH7.5, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.8 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.62 α = 90 b = 99.62 β = 90 c = 149.987 γ = 90
Symmetry Space Group P 41 21 2
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 ADSC CCD 2004-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.13 34.28 94.2 0.08 12.8 4 39329 1.5
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 2.13 2.21 53.8 0.48 1.9 3.5
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 1JST 2.15 83.05 37310 1984 94.2 0.185 0.181 0.1854 0.246 0.2456 RANDOM 45.24
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] 0.72 0.72 -1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.556 r_dihedral_angle_4_deg 18.457 r_dihedral_angle_3_deg 18.051 r_dihedral_angle_1_deg 6.585 r_scangle_it 3.258 r_scbond_it 2.232 r_angle_refined_deg 1.69 r_mcangle_it 1.411 r_mcbond_it 0.874 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.556 r_dihedral_angle_4_deg 18.457 r_dihedral_angle_3_deg 18.051 r_dihedral_angle_1_deg 6.585 r_scangle_it 3.258 r_scbond_it 2.232 r_angle_refined_deg 1.69 r_mcangle_it 1.411 r_mcbond_it 0.874 r_nbtor_refined 0.314 r_symmetry_vdw_refined 0.282 r_symmetry_hbond_refined 0.247 r_nbd_refined 0.239 r_xyhbond_nbd_refined 0.22 r_chiral_restr 0.122 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 4617 Nucleic Acid Atoms Solvent Atoms 547 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing