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CDK2-cyclin A in complex with FragLite 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GUC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 Protein at 10 mg/ml. 0.6 to 0.8 M KCl, 0.9 to 1.2 M (NH4)2SO4, and 100 mM HEPES pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.8 56.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.864 α = 90 b = 133.717 β = 90 c = 147.866 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 2020-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.89842 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.48 147.87 95 0.173 0.187 0.07 0.998 11.3 13.5 50159
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.48 2.56 1.225 1.32 0.491 0.779 14
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.48 99.375 50088 2559 95.074 0.202 0.2004 0.1969 0.2307 0.226 51.217
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] -1.338 -0.125 1.464
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.372 r_dihedral_angle_6_deg 16.399 r_dihedral_angle_3_deg 15.052 r_lrange_it 8.912 r_scangle_it 6.463 r_dihedral_angle_1_deg 6.058 r_mcangle_it 4.706 r_scbond_it 4.113 r_mcbond_it 2.878 r_angle_refined_deg 1.751
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.372 r_dihedral_angle_6_deg 16.399 r_dihedral_angle_3_deg 15.052 r_lrange_it 8.912 r_scangle_it 6.463 r_dihedral_angle_1_deg 6.058 r_mcangle_it 4.706 r_scbond_it 4.113 r_mcbond_it 2.878 r_angle_refined_deg 1.751 r_nbtor_refined 0.317 r_symmetry_xyhbond_nbd_refined 0.237 r_symmetry_nbd_refined 0.226 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.115 r_bond_refined_d 0.009 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8902 Nucleic Acid Atoms Solvent Atoms 414 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing