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CDK2 in complex with FragLite14
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 2.01 38.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.314 α = 90 b = 72.378 β = 90 c = 72.38 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 1.13 51.18 99.4 0.04 0.99 11.2 1.9 104589
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 1.13 1.15 96.3 1.81 0.24 0.6 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 1.13 51.18 99193 5396 99.21 0.18413 0.18217 0.1891 0.22044 0.226 RANDOM 20.425
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] 0.41 0.29 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.751 r_rigid_bond_restr 17.877 r_dihedral_angle_4_deg 15.631 r_dihedral_angle_3_deg 15.152 r_dihedral_angle_1_deg 6.208 r_long_range_B_refined 5.691 r_long_range_B_other 5.69 r_scangle_other 5.135 r_scbond_other 4.391 r_scbond_it 4.388
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.751 r_rigid_bond_restr 17.877 r_dihedral_angle_4_deg 15.631 r_dihedral_angle_3_deg 15.152 r_dihedral_angle_1_deg 6.208 r_long_range_B_refined 5.691 r_long_range_B_other 5.69 r_scangle_other 5.135 r_scbond_other 4.391 r_scbond_it 4.388 r_mcangle_it 4.185 r_mcangle_other 4.184 r_mcbond_it 3.501 r_mcbond_other 3.466 r_angle_other_deg 2.344 r_angle_refined_deg 2.052 r_chiral_restr 0.124 r_bond_other_d 0.033 r_gen_planes_other 0.024 r_bond_refined_d 0.016 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 2355 Nucleic Acid Atoms Solvent Atoms 298 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing