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Cdk2(F80C, C177A) with covalent adduct at C80
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 1.98 37.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.713 α = 90 b = 71.218 β = 90 c = 72.317 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 1.77 50.74 100 0.015 31.7 1.9 27188
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 1.77 1.81 99.9 0.048 12.6 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4EK3 1.77 50.7 25806 1381 99.94 0.16442 0.16217 0.20611 0.2188 RANDOM 22.042
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] 0.64 0.05 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.591 r_dihedral_angle_4_deg 19.132 r_dihedral_angle_3_deg 13.421 r_long_range_B_refined 6.854 r_dihedral_angle_1_deg 5.647 r_scbond_it 3.472 r_mcangle_it 3.401 r_mcbond_it 2.405 r_angle_refined_deg 2.199 r_chiral_restr 0.162
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.591 r_dihedral_angle_4_deg 19.132 r_dihedral_angle_3_deg 13.421 r_long_range_B_refined 6.854 r_dihedral_angle_1_deg 5.647 r_scbond_it 3.472 r_mcangle_it 3.401 r_mcbond_it 2.405 r_angle_refined_deg 2.199 r_chiral_restr 0.162 r_bond_refined_d 0.023 r_gen_planes_refined 0.014 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 2303 Nucleic Acid Atoms Solvent Atoms 332 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing