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Cdk2(F80C, C177A) with covalent ligand at F80C
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 9 - 15% w/v, 50 mM HEPES, 50 mM sodium/potassium phosphate
Crystal Properties Matthews coefficient Solvent content 1.99 38.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.11 α = 90 b = 70.97 β = 90 c = 72.43 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 2017-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.73 36.67 99.71 0.0853 0.9993 13.82 7.19 29150
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.73 1.76 99.86 1.6585 0.5609 1.07 7.4
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 1.73 36.67 27745 1404 99.7 0.18729 0.1843 0.1884 0.2491 0.2538 RANDOM 33.251
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] 3.03 -2.28 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.894 r_dihedral_angle_4_deg 20.651 r_dihedral_angle_3_deg 14.662 r_long_range_B_refined 9.01 r_dihedral_angle_1_deg 5.536 r_scbond_it 4.281 r_mcangle_it 4.117 r_mcbond_it 2.996 r_angle_refined_deg 1.891 r_chiral_restr 0.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.894 r_dihedral_angle_4_deg 20.651 r_dihedral_angle_3_deg 14.662 r_long_range_B_refined 9.01 r_dihedral_angle_1_deg 5.536 r_scbond_it 4.281 r_mcangle_it 4.117 r_mcbond_it 2.996 r_angle_refined_deg 1.891 r_chiral_restr 0.129 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 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 2284 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing