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Structure of Fully modified farnesylated Rheb Peptide in complex with PDE6D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3T5G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293 0.1 MES 6.5 and 30 % PEG 5000 MME , pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.25 45.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.75 α = 90 b = 70.05 β = 81.55 c = 71.23 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 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 2.1 30 99.6 37401 1 1
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 2.1 2.2 99.5
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 3T5G 2.1 29.91 1 35530 35530 1870 100 0.19137 0.19137 0.18867 0.1901 0.24309 0.2448 RANDOM 28.721
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] -0.46 0.08 -0.38 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.804 r_dihedral_angle_4_deg 16.089 r_dihedral_angle_3_deg 15.39 r_dihedral_angle_1_deg 6.377 r_scangle_it 3.721 r_scbond_it 2.196 r_mcangle_it 1.415 r_angle_refined_deg 1.384 r_mcbond_it 0.73 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.804 r_dihedral_angle_4_deg 16.089 r_dihedral_angle_3_deg 15.39 r_dihedral_angle_1_deg 6.377 r_scangle_it 3.721 r_scbond_it 2.196 r_mcangle_it 1.415 r_angle_refined_deg 1.384 r_mcbond_it 0.73 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4799 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 60
Software Software Software Name Purpose ProDC data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling