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Truncation and Optimisation of Peptide Inhibitors of CDK2, Cyclin A Through Structure Guided Design
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OL1 PDB ENTRY 1OL1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.8 PEG3350 30% V/V, 0.1M TRI-SODIUM CITRATE, pH 7.8
Crystal Properties Matthews coefficient Solvent content 2.48 50.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.523 α = 90 b = 113.844 β = 90 c = 158.462 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 CCD ADSC CCD MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.3 40 96.4 0.09 15.7 4.1 60655 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.42 80.4 0.28
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1OL1 2.3 40 55318 2926 96.05 0.18992 0.1871 0.2427 0.2463 RANDOM 29.276
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] 1.73 -0.92 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.512 r_dihedral_angle_3_deg 15.65 r_dihedral_angle_4_deg 14.814 r_dihedral_angle_1_deg 6.798 r_scangle_it 4.281 r_scbond_it 2.878 r_mcangle_it 1.974 r_angle_refined_deg 1.354 r_mcbond_it 1.2 r_angle_other_deg 0.895
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.512 r_dihedral_angle_3_deg 15.65 r_dihedral_angle_4_deg 14.814 r_dihedral_angle_1_deg 6.798 r_scangle_it 4.281 r_scbond_it 2.878 r_mcangle_it 1.974 r_angle_refined_deg 1.354 r_mcbond_it 1.2 r_angle_other_deg 0.895 r_mcbond_other 0.282 r_symmetry_hbond_refined 0.267 r_nbd_refined 0.219 r_xyhbond_nbd_other 0.215 r_nbd_other 0.21 r_symmetry_vdw_other 0.209 r_symmetry_vdw_refined 0.204 r_xyhbond_nbd_refined 0.2 r_nbtor_refined 0.185 r_nbtor_other 0.094 r_chiral_restr 0.088 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9017 Nucleic Acid Atoms Solvent Atoms 545 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing