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CDK2 in complex with FragLite1
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 37.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.439 α = 90 b = 71.333 β = 90 c = 71.886 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 2016-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.919 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 1.29 50.63 88.5 0.13 0.99 8.3 6.6 61548
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.29 1.31 46.1 0.43 1.5 4.5
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 1.29 50.63 58568 2980 88.14 0.14237 0.1405 0.1416 0.17813 0.1424 RANDOM 25.147
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] -0.46 0.77 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.647 r_dihedral_angle_3_deg 15.474 r_dihedral_angle_4_deg 15.263 r_rigid_bond_restr 13.289 r_long_range_B_refined 6.879 r_long_range_B_other 6.878 r_dihedral_angle_1_deg 6.108 r_scangle_other 5.846 r_mcangle_it 4.863 r_mcangle_other 4.863
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.647 r_dihedral_angle_3_deg 15.474 r_dihedral_angle_4_deg 15.263 r_rigid_bond_restr 13.289 r_long_range_B_refined 6.879 r_long_range_B_other 6.878 r_dihedral_angle_1_deg 6.108 r_scangle_other 5.846 r_mcangle_it 4.863 r_mcangle_other 4.863 r_scbond_it 4.841 r_scbond_other 4.839 r_mcbond_it 4.674 r_mcbond_other 4.669 r_angle_other_deg 2.301 r_angle_refined_deg 1.755 r_chiral_restr 0.1 r_bond_other_d 0.033 r_gen_planes_other 0.016 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 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 2334 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing