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CO-CRYSTAL STRUCTURE OF RAT PROTEIN FARNESYLTRANSFERASE COMPLEXED WITH A-176120
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D8D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 0.1 M citric pH 5 and 0.8M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.27 62.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 172.777 α = 90 b = 172.777 β = 90 c = 70.489 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 100 PIXEL DECTRIS EIGER X 9M 2023-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87313 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.31 44.15 100 1 21.9 20.3 52888
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 2.31 2.39 100 1.709 1.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.31 44.15 50259 2604 99.98 0.22885 0.22765 0.2342 0.2513 0.2562 RANDOM 68.089
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] -0.23 -0.11 -0.23 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.196 r_long_range_B_other 6.612 r_long_range_B_refined 6.611 r_dihedral_angle_1_deg 5.565 r_scangle_other 4.428 r_mcangle_it 4.311 r_mcangle_other 4.31 r_dihedral_angle_2_deg 3.82 r_mcbond_it 2.656 r_mcbond_other 2.655
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.196 r_long_range_B_other 6.612 r_long_range_B_refined 6.611 r_dihedral_angle_1_deg 5.565 r_scangle_other 4.428 r_mcangle_it 4.311 r_mcangle_other 4.31 r_dihedral_angle_2_deg 3.82 r_mcbond_it 2.656 r_mcbond_other 2.655 r_scbond_it 2.583 r_scbond_other 2.583 r_angle_refined_deg 0.979 r_angle_other_deg 0.373 r_chiral_restr 0.049 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5688 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing