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CDK2 in complex with FragLite38
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 1.95 37.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.897 α = 90 b = 71.265 β = 90 c = 72.062 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 2017-07-05 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 72.07 84.3 0.026 0.99 24.7 5.7 105138
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 5.5 0.56 0.61 0.8 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 50.72 99908 5230 84.27 0.14407 0.14312 0.1425 0.16216 0.1616 RANDOM 19.66
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] -0.56 0.59 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.591 r_dihedral_angle_4_deg 13.813 r_dihedral_angle_3_deg 13.282 r_rigid_bond_restr 11.882 r_dihedral_angle_1_deg 6.185 r_long_range_B_refined 4.673 r_long_range_B_other 4.673 r_scangle_other 4.041 r_scbond_it 3.343 r_scbond_other 3.342
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.591 r_dihedral_angle_4_deg 13.813 r_dihedral_angle_3_deg 13.282 r_rigid_bond_restr 11.882 r_dihedral_angle_1_deg 6.185 r_long_range_B_refined 4.673 r_long_range_B_other 4.673 r_scangle_other 4.041 r_scbond_it 3.343 r_scbond_other 3.342 r_mcangle_it 2.99 r_mcangle_other 2.989 r_angle_other_deg 2.321 r_mcbond_it 2.317 r_mcbond_other 2.312 r_angle_refined_deg 1.881 r_chiral_restr 0.109 r_bond_other_d 0.033 r_gen_planes_other 0.016 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 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 2358 Nucleic Acid Atoms Solvent Atoms 317 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing