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CDK2 in complex with FragLite32
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 37.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.187 α = 90 b = 71.467 β = 90 c = 72.042 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 1.21 72.04 99.9 0.04 0.99 15.3 6.6 84174
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 1.21 1.23 97.7 0.68 0.31 1 3.7
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 1.21 50.79 80037 4137 99.81 0.16914 0.16732 0.1747 0.20515 0.212 RANDOM 25.927
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] -0.85 -0.38 1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.431 r_rigid_bond_restr 16.983 r_dihedral_angle_4_deg 16.374 r_dihedral_angle_3_deg 15.09 r_long_range_B_refined 7.052 r_long_range_B_other 7.051 r_scangle_other 6.458 r_dihedral_angle_1_deg 6.023 r_scbond_it 5.577 r_scbond_other 5.575
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.431 r_rigid_bond_restr 16.983 r_dihedral_angle_4_deg 16.374 r_dihedral_angle_3_deg 15.09 r_long_range_B_refined 7.052 r_long_range_B_other 7.051 r_scangle_other 6.458 r_dihedral_angle_1_deg 6.023 r_scbond_it 5.577 r_scbond_other 5.575 r_mcangle_other 4.897 r_mcangle_it 4.892 r_mcbond_it 3.914 r_mcbond_other 3.9 r_angle_other_deg 2.335 r_angle_refined_deg 1.996 r_chiral_restr 0.115 r_bond_other_d 0.033 r_gen_planes_other 0.019 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 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 2366 Nucleic Acid Atoms Solvent Atoms 310 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing