☰ Navigation Tabs
CDK2 in complex with FragLite33
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 38.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.188 α = 90 b = 72.431 β = 90 c = 71.94 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 2018-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.98 Diamond I04
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 1.06 72.43 84.9 0.11 0.99 9.1 5.6 107335
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 1.06 1.08 5.6 0.5 0.76 0.7 1.1
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 1.06 51.09 102042 5293 84.92 0.18034 0.17901 0.1888 0.20514 0.2125 RANDOM 19.395
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] 1.02 -1.53 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.847 r_rigid_bond_restr 20.022 r_dihedral_angle_4_deg 17.603 r_dihedral_angle_3_deg 15.095 r_dihedral_angle_1_deg 5.963 r_long_range_B_refined 4.707 r_long_range_B_other 4.706 r_scangle_other 4.328 r_scbond_other 3.406 r_scbond_it 3.405
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.847 r_rigid_bond_restr 20.022 r_dihedral_angle_4_deg 17.603 r_dihedral_angle_3_deg 15.095 r_dihedral_angle_1_deg 5.963 r_long_range_B_refined 4.707 r_long_range_B_other 4.706 r_scangle_other 4.328 r_scbond_other 3.406 r_scbond_it 3.405 r_mcangle_it 3.325 r_mcangle_other 3.324 r_mcbond_it 3.047 r_mcbond_other 3.046 r_angle_other_deg 2.325 r_angle_refined_deg 1.997 r_chiral_restr 0.116 r_bond_other_d 0.033 r_gen_planes_other 0.021 r_bond_refined_d 0.015 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 2290 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing