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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 18% V/V PEG3350 AND 0.1M SODIUM CITRATE, pH 7.8
Crystal Properties Matthews coefficient Solvent content 2.48 50.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.423 α = 90 b = 114.924 β = 90 c = 154.468 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 2004-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.9 30 98 0.12 4.4 3.5 29405 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 2.9 3.06 96.2 0.67 1.6
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 1OL1 2.9 30 28324 944 97.36 0.1887 0.18614 0.1931 0.26393 0.2682 RANDOM 43.787
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] -1.7 0.34 1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.543 r_dihedral_angle_3_deg 21.668 r_dihedral_angle_4_deg 21.414 r_scangle_it 8.191 r_dihedral_angle_1_deg 7.95 r_scbond_it 5.561 r_mcangle_it 3.718 r_angle_refined_deg 2.589 r_mcbond_it 2.375 r_angle_other_deg 1.258
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.543 r_dihedral_angle_3_deg 21.668 r_dihedral_angle_4_deg 21.414 r_scangle_it 8.191 r_dihedral_angle_1_deg 7.95 r_scbond_it 5.561 r_mcangle_it 3.718 r_angle_refined_deg 2.589 r_mcbond_it 2.375 r_angle_other_deg 1.258 r_mcbond_other 0.532 r_nbd_refined 0.253 r_symmetry_hbond_refined 0.25 r_nbd_other 0.234 r_nbtor_refined 0.213 r_symmetry_vdw_other 0.208 r_xyhbond_nbd_refined 0.207 r_symmetry_vdw_refined 0.143 r_xyhbond_nbd_other 0.134 r_chiral_restr 0.133 r_nbtor_other 0.113 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 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 9013 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing