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CDK2 in complex with FragLite2
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 1.97 37.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.33 α = 90 b = 71.36 β = 90 c = 72.01 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 2016-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.98 Diamond I03
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 1.18 50.74 99.9 0.02 0.99 14.7 1.9 90732
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 1.18 1.2 99.5 0.66 0.47 1.3 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 1HCK 1.18 50.74 86255 4477 99.8 0.16276 0.1613 0.1706 0.18857 0.1765 RANDOM 25.539
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 0.17 1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.937 r_rigid_bond_restr 23.278 r_dihedral_angle_4_deg 17.516 r_dihedral_angle_3_deg 14.676 r_mcangle_other 13.695 r_mcangle_it 13.529 r_mcbond_it 10.82 r_mcbond_other 10.28 r_scangle_other 10.205 r_long_range_B_refined 10.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.937 r_rigid_bond_restr 23.278 r_dihedral_angle_4_deg 17.516 r_dihedral_angle_3_deg 14.676 r_mcangle_other 13.695 r_mcangle_it 13.529 r_mcbond_it 10.82 r_mcbond_other 10.28 r_scangle_other 10.205 r_long_range_B_refined 10.178 r_long_range_B_other 10.176 r_scbond_it 7.89 r_scbond_other 7.887 r_dihedral_angle_1_deg 5.617 r_angle_other_deg 2.365 r_angle_refined_deg 2.154 r_chiral_restr 0.126 r_bond_other_d 0.033 r_gen_planes_other 0.026 r_bond_refined_d 0.017 r_gen_planes_refined 0.014 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 2364 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing