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Cdk2(WT) with covalent adduct at C177
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EK3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 15% w/v Jeffamine ED-2003, 50 mM HEPES, 50 mM sodium/potassium phosphate
Crystal Properties Matthews coefficient Solvent content 2.01 38.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.916 α = 90 b = 71.111 β = 90 c = 72.25 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 ADSC QUANTUM 315 2017-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 1.83 50.68 99.9 0.028 16.5 1.9 25118
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 1.83 1.87 99 0.245 3.3 1.9
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 4EK3 1.83 50.3 23782 1335 99.83 0.17625 0.17378 0.1736 0.22198 0.2213 RANDOM 22.214
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 0.84 -0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.466 r_dihedral_angle_4_deg 17.269 r_dihedral_angle_3_deg 13.143 r_long_range_B_refined 7.045 r_dihedral_angle_1_deg 5.574 r_scbond_it 3.279 r_mcangle_it 3.118 r_mcbond_it 2.132 r_angle_refined_deg 1.92 r_chiral_restr 0.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.466 r_dihedral_angle_4_deg 17.269 r_dihedral_angle_3_deg 13.143 r_long_range_B_refined 7.045 r_dihedral_angle_1_deg 5.574 r_scbond_it 3.279 r_mcangle_it 3.118 r_mcbond_it 2.132 r_angle_refined_deg 1.92 r_chiral_restr 0.133 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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_it r_scangle_other 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 2291 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing