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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 1OKV PDB ENTRY 1OKV
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 = 74.621 α = 90 b = 115.813 β = 90 c = 157.911 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 SRS BEAMLINE PX14.1 SRS PX14.1
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 2.53 40 80 0.3 9 13 46387 1.3
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 2.53 2.56 70 0.3 1.34
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 PDB ENTRY 1OKV 2.53 40 41853 880 92.17 0.19466 0.19328 0.1919 0.25878 0.254 RANDOM 52.652
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] -3.49 1 2.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.514 r_dihedral_angle_4_deg 22.41 r_dihedral_angle_3_deg 20.113 r_dihedral_angle_1_deg 6.764 r_scangle_it 5.578 r_scbond_it 3.692 r_mcangle_it 2.262 r_angle_refined_deg 1.608 r_mcbond_it 1.411 r_nbtor_refined 0.327
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.514 r_dihedral_angle_4_deg 22.41 r_dihedral_angle_3_deg 20.113 r_dihedral_angle_1_deg 6.764 r_scangle_it 5.578 r_scbond_it 3.692 r_mcangle_it 2.262 r_angle_refined_deg 1.608 r_mcbond_it 1.411 r_nbtor_refined 0.327 r_nbd_refined 0.244 r_symmetry_vdw_refined 0.226 r_xyhbond_nbd_refined 0.195 r_symmetry_hbond_refined 0.161 r_chiral_restr 0.114 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_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 443 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing