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REPLACE: A strategy for Iterative Design of Cyclin Binding Groove Inhibitors
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 22% PEG 3350, 0.1M NA3-CIT, pH 7.80
Crystal Properties Matthews coefficient Solvent content 2.7 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.563 α = 90 b = 113.8 β = 90 c = 155.031 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 2003-02-14 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 2.06 20 99 0.11 13.2 2.3 79118 13.2
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 2.06 2.17 98 1.06 1.4
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 2.06 91.29 78456 2431 98.8 0.197 0.196 0.199 0.244 0.2445 RANDOM 54.14
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] -2.06 0.99 1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.401 r_dihedral_angle_4_deg 22.739 r_dihedral_angle_3_deg 20.848 r_scangle_it 9.899 r_dihedral_angle_1_deg 7.902 r_scbond_it 7.005 r_mcangle_it 4.519 r_mcbond_it 2.995 r_angle_refined_deg 1.636 r_nbtor_refined 0.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.401 r_dihedral_angle_4_deg 22.739 r_dihedral_angle_3_deg 20.848 r_scangle_it 9.899 r_dihedral_angle_1_deg 7.902 r_scbond_it 7.005 r_mcangle_it 4.519 r_mcbond_it 2.995 r_angle_refined_deg 1.636 r_nbtor_refined 0.332 r_symmetry_hbond_refined 0.323 r_nbd_refined 0.258 r_symmetry_vdw_refined 0.247 r_xyhbond_nbd_refined 0.198 r_chiral_restr 0.146 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 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 9004 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing