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CDK2 in complex with FragLite6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HCK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 10MG/ML CDK2 10% V/V PEG3350, 50 MM HEPES/NAOH, 50 MM NA/K PHOSPHATE, PH 7.5
Crystal Properties Matthews coefficient Solvent content 1.99 38.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.069 α = 90 b = 72.53 β = 90 c = 71.899 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 PIXEL DECTRIS PILATUS 6M 2017-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.916 Diamond I04-1
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 72.53 99.9 0.05 0.99 11.4 6.6 149763
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 1.02 99.3 1.91 0.28 0.6 4.3
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 1HCK 1 42.87 142358 7405 99.87 0.17629 0.17524 0.1839 0.19718 0.2061 RANDOM 23.835
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] 0.11 0.09 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.941 r_rigid_bond_restr 25.357 r_mcbond_other 16.576 r_mcbond_it 16.569 r_mcangle_it 16.007 r_mcangle_other 16.001 r_long_range_B_refined 15.752 r_long_range_B_other 15.749 r_dihedral_angle_3_deg 14.768 r_dihedral_angle_4_deg 14.684
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.941 r_rigid_bond_restr 25.357 r_mcbond_other 16.576 r_mcbond_it 16.569 r_mcangle_it 16.007 r_mcangle_other 16.001 r_long_range_B_refined 15.752 r_long_range_B_other 15.749 r_dihedral_angle_3_deg 14.768 r_dihedral_angle_4_deg 14.684 r_scangle_other 14.673 r_scbond_it 11.907 r_scbond_other 11.902 r_dihedral_angle_1_deg 6.031 r_angle_other_deg 2.317 r_angle_refined_deg 2.15 r_chiral_restr 0.136 r_bond_other_d 0.033 r_gen_planes_other 0.027 r_bond_refined_d 0.018 r_gen_planes_refined 0.013 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2307 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing