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CDK1/Cks2 in complex with Dinaciclib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YC6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 CONDITIONS AROUND 0.1M BIS-TRIS(PH6.5), 0.2M SODIUM NITRATE 20% PEG3350, PROTEIN AT 10-12 MG/ML, 0.5Mm INHIBITOR
Crystal Properties Matthews coefficient Solvent content 2.76 55.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.704 α = 90 b = 97.232 β = 90 c = 108.564 γ = 90
Symmetry Space Group I 2 2 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 PIXEL DECTRIS PILATUS 6M 2016-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.987 Diamond I24
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 2.33 72.43 99.8 0.05 10.8 1.9 21580
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 2.33 2.41 97.7 0.42 2.4 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 4YC6 2.33 72.43 20503 1077 99.78 0.20317 0.20092 0.2043 0.24586 0.2457 RANDOM 47.498
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] 1.9 -1.73 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.208 r_dihedral_angle_4_deg 20.6 r_dihedral_angle_3_deg 18.415 r_long_range_B_other 9.98 r_long_range_B_refined 9.975 r_dihedral_angle_1_deg 7.635 r_scangle_other 7.605 r_mcangle_it 6.103 r_mcangle_other 6.101 r_scbond_it 4.905
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.208 r_dihedral_angle_4_deg 20.6 r_dihedral_angle_3_deg 18.415 r_long_range_B_other 9.98 r_long_range_B_refined 9.975 r_dihedral_angle_1_deg 7.635 r_scangle_other 7.605 r_mcangle_it 6.103 r_mcangle_other 6.101 r_scbond_it 4.905 r_scbond_other 4.905 r_mcbond_other 4.049 r_mcbond_it 4.048 r_angle_other_deg 3.598 r_angle_refined_deg 1.85 r_chiral_restr 0.117 r_bond_refined_d 0.016 r_gen_planes_other 0.009 r_gen_planes_refined 0.008 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2943 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing