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Structure of Fully modified geranylgeranylated PDE6C 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, SITTING DROP 293 0.1 M HEPES (pH 7.5), 0.2 M Li2SO4, 25 % PEG4000 and 0.1 M NaOAc
Crystal Properties Matthews coefficient Solvent content 2.61 52.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.71 α = 90 b = 81.43 β = 90 c = 118.53 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS PILATUS 6M 2014-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00001 SLS X10SA
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 2.1 29.63 99.6 0.05 23.46 5.29 22232
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.2 100 0.163 10.24 5.35
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3T5G 2.1 29.63 21194 1116 99.95 0.2012 0.1983 0.2032 0.2561 0.2585 RANDOM 34.13
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] 0.9 0.11 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.02 r_dihedral_angle_3_deg 16.095 r_dihedral_angle_4_deg 15.022 r_dihedral_angle_1_deg 7.093 r_mcangle_it 3.726 r_mcbond_it 2.82 r_mcbond_other 2.82 r_angle_refined_deg 1.973 r_angle_other_deg 0.992 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.02 r_dihedral_angle_3_deg 16.095 r_dihedral_angle_4_deg 15.022 r_dihedral_angle_1_deg 7.093 r_mcangle_it 3.726 r_mcbond_it 2.82 r_mcbond_other 2.82 r_angle_refined_deg 1.973 r_angle_other_deg 0.992 r_chiral_restr 0.112 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2543 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing Coot model building