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CDK2 in complex with FragLite35
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 2 38.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.314 α = 90 b = 72.573 β = 90 c = 72.038 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 2018-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.98 Diamond I24
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 1.11 53.31 89.8 0.08 0.99 11.4 6.1 99386
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 1.11 1.13 44.3 0.77 0.55 1.4 2.6
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 1.11 51.18 94432 4954 89.72 0.16624 0.16487 0.1738 0.19246 0.1987 RANDOM 16.638
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] 0.86 -0.37 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.779 r_rigid_bond_restr 17.525 r_dihedral_angle_3_deg 14.333 r_dihedral_angle_4_deg 14.291 r_dihedral_angle_1_deg 6.111 r_long_range_B_refined 3.869 r_long_range_B_other 3.868 r_scangle_other 3.456 r_mcangle_it 2.759 r_mcangle_other 2.758
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.779 r_rigid_bond_restr 17.525 r_dihedral_angle_3_deg 14.333 r_dihedral_angle_4_deg 14.291 r_dihedral_angle_1_deg 6.111 r_long_range_B_refined 3.869 r_long_range_B_other 3.868 r_scangle_other 3.456 r_mcangle_it 2.759 r_mcangle_other 2.758 r_scbond_other 2.727 r_scbond_it 2.726 r_angle_other_deg 2.309 r_mcbond_it 2.106 r_mcbond_other 2.093 r_angle_refined_deg 1.895 r_chiral_restr 0.114 r_bond_other_d 0.034 r_gen_planes_other 0.016 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 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 2330 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing