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Cocrystal structure of PDE6D bound to NRAS peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TB5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 279 0.1 M citric acid pH 4.0 and 3.2 M AmSO4
Crystal Properties Matthews coefficient Solvent content 3.02 59.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.788 α = 90 b = 55.788 β = 90 c = 114.842 γ = 120
Symmetry Space Group P 32 2 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 PIXEL DECTRIS EIGER X 16M 2019-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
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 2.5 114.87 100 0.995 10.5 9.5 7634
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.56 0.859
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5TB5 2.5 48.36 7602 346 99.974 0.235 0.2335 0.2362 0.2759 0.2749 28.585
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] 0.731 0.366 0.731 -2.373
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.145 r_dihedral_angle_4_deg 17.789 r_dihedral_angle_3_deg 15.165 r_dihedral_angle_1_deg 6.695 r_lrange_it 2.696 r_lrange_other 2.687 r_mcangle_it 1.169 r_mcangle_other 1.168 r_angle_refined_deg 1.016 r_angle_other_deg 0.997
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.145 r_dihedral_angle_4_deg 17.789 r_dihedral_angle_3_deg 15.165 r_dihedral_angle_1_deg 6.695 r_lrange_it 2.696 r_lrange_other 2.687 r_mcangle_it 1.169 r_mcangle_other 1.168 r_angle_refined_deg 1.016 r_angle_other_deg 0.997 r_scangle_it 0.668 r_scangle_other 0.668 r_mcbond_it 0.618 r_mcbond_other 0.618 r_scbond_it 0.327 r_scbond_other 0.325 r_nbd_other 0.285 r_symmetry_nbd_other 0.223 r_symmetry_nbd_refined 0.202 r_nbd_refined 0.201 r_xyhbond_nbd_refined 0.19 r_nbtor_refined 0.16 r_symmetry_xyhbond_nbd_refined 0.096 r_symmetry_xyhbond_nbd_other 0.081 r_symmetry_nbtor_other 0.07 r_chiral_restr 0.019 r_gen_planes_refined 0.002 r_bond_refined_d 0.001 r_gen_planes_other 0.001 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1197 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing