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Structure of fully modified farnesylated Rheb in complex with PDE6D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XTQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293 0.1 M Tris 8.5, and 12.5 % PEG8000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.44 49.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.89 α = 90 b = 57.38 β = 90 c = 134.52 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 MARMOSAIC 225 mm CCD 2010-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.979 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 30 97.2 40454 40454 1 1
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 1.7 1.8 95.7 0.28 5.95 6.7 6158
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1XTQ 1.7 29.01 1 38429 38429 2023 100 0.19944 0.19944 0.19757 0.197 0.23538 0.2352 RANDOM 19.637
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] -0.11 0.66 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.091 r_dihedral_angle_3_deg 11.983 r_dihedral_angle_4_deg 8.856 r_dihedral_angle_1_deg 5.641 r_scangle_it 2.699 r_scbond_it 1.606 r_mcangle_it 1.092 r_angle_refined_deg 1.078 r_mcbond_it 0.568 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.091 r_dihedral_angle_3_deg 11.983 r_dihedral_angle_4_deg 8.856 r_dihedral_angle_1_deg 5.641 r_scangle_it 2.699 r_scbond_it 1.606 r_mcangle_it 1.092 r_angle_refined_deg 1.078 r_mcbond_it 0.568 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2549 Nucleic Acid Atoms Solvent Atoms 416 Heterogen Atoms 44
Software Software Software Name Purpose ProDC data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling