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CDK2 in complex with FragLite16
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 1.96 37.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.963 α = 90 b = 71.491 β = 90 c = 71.97 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 IMAGE PLATE MAR scanner 300 mm plate 2016-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
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 42.66 93.6 0.023 1 29.7 3.2 26999
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 86.9 0.3 0.88 3.2 2.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1HCK 1.73 29.78 25698 1301 92.22 0.1821 0.17999 0.22267 0.2239 RANDOM 28.759
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] 0.22 0.65 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.22 r_dihedral_angle_3_deg 15.051 r_dihedral_angle_4_deg 14.885 r_long_range_B_refined 7.168 r_long_range_B_other 7.167 r_dihedral_angle_1_deg 6.65 r_scangle_other 4.992 r_mcangle_it 3.723 r_mcangle_other 3.722 r_scbond_it 3.187
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.22 r_dihedral_angle_3_deg 15.051 r_dihedral_angle_4_deg 14.885 r_long_range_B_refined 7.168 r_long_range_B_other 7.167 r_dihedral_angle_1_deg 6.65 r_scangle_other 4.992 r_mcangle_it 3.723 r_mcangle_other 3.722 r_scbond_it 3.187 r_scbond_other 3.186 r_mcbond_it 2.588 r_mcbond_other 2.585 r_angle_other_deg 2.305 r_angle_refined_deg 1.586 r_chiral_restr 0.085 r_bond_other_d 0.034 r_gen_planes_other 0.012 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 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 2367 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing