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Crystal structure of PDE6D in complex with Compound-2
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, HANGING DROP 291 1.2 M AmSO4 and 0.1 M ammonium acetate pH 4.9 at 291K
Crystal Properties Matthews coefficient Solvent content 2.56 51.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.548 α = 90 b = 76.548 β = 90 c = 238.018 γ = 90
Symmetry Space Group P 41 21 2
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 2019-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97951 Diamond I04
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 3.1 76.55 90.6 0.975 5.6 8 12108
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 3.1 3.31 0.343
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 3.1 64.463 12095 625 88.829 0.248 0.2464 0.2452 0.2831 0.2762 76.627
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] -0.979 -0.979 1.958
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.758 r_dihedral_angle_3_deg 19.209 r_dihedral_angle_4_deg 17.759 r_lrange_it 10.666 r_lrange_other 10.665 r_scangle_it 7.244 r_scangle_other 7.242 r_mcangle_it 6.668 r_mcangle_other 6.667 r_dihedral_angle_1_deg 5.988
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.758 r_dihedral_angle_3_deg 19.209 r_dihedral_angle_4_deg 17.759 r_lrange_it 10.666 r_lrange_other 10.665 r_scangle_it 7.244 r_scangle_other 7.242 r_mcangle_it 6.668 r_mcangle_other 6.667 r_dihedral_angle_1_deg 5.988 r_scbond_it 4.284 r_scbond_other 4.282 r_mcbond_it 4.159 r_mcbond_other 4.153 r_chiral_restr_other 2.517 r_angle_other_deg 1.105 r_angle_refined_deg 1.091 r_nbd_other 0.307 r_symmetry_nbd_refined 0.306 r_symmetry_nbd_other 0.221 r_ncsr_local_group_6 0.213 r_ncsr_local_group_5 0.212 r_nbd_refined 0.209 r_ncsr_local_group_3 0.209 r_symmetry_xyhbond_nbd_refined 0.208 r_ncsr_local_group_4 0.182 r_ncsr_local_group_2 0.181 r_ncsr_local_group_1 0.178 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.17 r_symmetry_nbtor_other 0.076 r_symmetry_xyhbond_nbd_other 0.054 r_chiral_restr 0.034 r_bond_refined_d 0.002 r_bond_other_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4674 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing