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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 20% 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 = 74.558 α = 90 b = 114.257 β = 90 c = 157.277 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 2003-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.75 30 98.3 0.14 12.7 3.8 37669 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 2.75 2.9 98.8 0.67 1.9
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 2.75 30 33849 1097 98.01 0.20136 0.19964 0.2038 0.25478 0.2537 RANDOM 34.816
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] -2.38 -0.22 2.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.975 r_dihedral_angle_4_deg 17.162 r_dihedral_angle_3_deg 16.507 r_scangle_it 7.734 r_scbond_it 5.524 r_dihedral_angle_1_deg 5.167 r_mcangle_it 3.218 r_mcbond_it 2.284 r_angle_refined_deg 1.548 r_angle_other_deg 1.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.975 r_dihedral_angle_4_deg 17.162 r_dihedral_angle_3_deg 16.507 r_scangle_it 7.734 r_scbond_it 5.524 r_dihedral_angle_1_deg 5.167 r_mcangle_it 3.218 r_mcbond_it 2.284 r_angle_refined_deg 1.548 r_angle_other_deg 1.129 r_mcbond_other 0.473 r_symmetry_vdw_other 0.377 r_symmetry_hbond_refined 0.253 r_nbd_other 0.227 r_nbd_refined 0.219 r_symmetry_vdw_refined 0.193 r_nbtor_refined 0.189 r_xyhbond_nbd_other 0.184 r_xyhbond_nbd_refined 0.182 r_chiral_restr 0.092 r_nbtor_other 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.007 r_bond_other_d 0.006 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 8956 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing