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Structure of doubly prenylated Ypt1:GDI complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UKV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.9 293 14% PEG MME 2000,
100 mM Tris-Acetate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.33 47.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.66 α = 90 b = 120.23 β = 90.67 c = 60.55 γ = 90
Symmetry Space Group P 1 21 1
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 QUANTUM 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.934 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.48 19.92 96.5 0.076 11.32 113100 109178 -3 -3 24
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.48 1.49 75.1
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 1ukv 1.48 19.92 109178 103719 5459 96.5 0.16486 0.16486 0.16336 0.1612 0.19283 0.1912 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.495 r_dihedral_angle_4_deg 18.665 r_dihedral_angle_3_deg 13.621 r_dihedral_angle_1_deg 5.76 r_sphericity_free 5.636 r_sphericity_bonded 3.804 r_scangle_it 3.696 r_scbond_it 2.919 r_rigid_bond_restr 2.137 r_mcangle_it 2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.495 r_dihedral_angle_4_deg 18.665 r_dihedral_angle_3_deg 13.621 r_dihedral_angle_1_deg 5.76 r_sphericity_free 5.636 r_sphericity_bonded 3.804 r_scangle_it 3.696 r_scbond_it 2.919 r_rigid_bond_restr 2.137 r_mcangle_it 2 r_angle_refined_deg 1.453 r_mcbond_it 1.345 r_nbtor_refined 0.307 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.163 r_xyhbond_nbd_refined 0.148 r_symmetry_hbond_refined 0.123 r_chiral_restr 0.096 r_bond_refined_d 0.013 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5268 Nucleic Acid Atoms Solvent Atoms 923 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement ProDC data collection XDS data scaling