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General Structure-Based Approach to the Design of Protein Ligands: Application to the Design of Kv1.2 Potassium Channel Blockers.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J75 PDB ENTRY 1J75
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 25% PEG 4000, 0.2M Na/K phosphate, 0.1M MES, 5mM Bmercapto-ethanol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.64 53.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.91 α = 90 b = 79.91 β = 90 c = 55.335 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 2005-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.7 65 99.9 0.082 0.082 16.1 7 22226 1 1 25.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.79 100 0.417 0.417 3.1 7 3227
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1J75 1.7 20 22241 21057 1129 99.82 0.2414 0.248 0.241 0.2444 0.30507 0.304 RANDOM 34.061
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] 0.51 0.25 0.51 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.543 r_dihedral_angle_4_deg 21.039 r_dihedral_angle_3_deg 18.332 r_dihedral_angle_1_deg 5.198 r_scangle_it 2.695 r_angle_refined_deg 2.007 r_scbond_it 2.002 r_mcangle_it 1.314 r_mcbond_it 0.85 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.543 r_dihedral_angle_4_deg 21.039 r_dihedral_angle_3_deg 18.332 r_dihedral_angle_1_deg 5.198 r_scangle_it 2.695 r_angle_refined_deg 2.007 r_scbond_it 2.002 r_mcangle_it 1.314 r_mcbond_it 0.85 r_nbtor_refined 0.303 r_nbd_refined 0.277 r_symmetry_hbond_refined 0.268 r_xyhbond_nbd_refined 0.219 r_symmetry_vdw_refined 0.208 r_chiral_restr 0.158 r_bond_refined_d 0.013 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 924 Nucleic Acid Atoms 246 Solvent Atoms 228 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOLREP phasing