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Crystal structure of PDE6D Geranylgeranylated cystein complex
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 277 30% w/v PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.13 42.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.048 α = 77.725 b = 35.289 β = 68.98 c = 37.645 γ = 69.228
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 EIGER2 X 16M 2019-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 1 NSLS X6A
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 1.45 34.971 95.9 1 17.98 3.5 24436
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 1.45 1.49 0.669
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 1.45 34.971 24436 1222 96.193 0.228 0.2251 0.2335 0.2736 0.2751 29.697
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] -1.546 0.939 -0.111 0.583 -0.592 1.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.333 r_dihedral_angle_3_deg 15.033 r_dihedral_angle_4_deg 8.193 r_dihedral_angle_1_deg 6.659 r_lrange_it 6.14 r_lrange_other 6.117 r_scangle_it 4.751 r_scangle_other 4.749 r_mcangle_it 3.376 r_mcangle_other 3.376
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.333 r_dihedral_angle_3_deg 15.033 r_dihedral_angle_4_deg 8.193 r_dihedral_angle_1_deg 6.659 r_lrange_it 6.14 r_lrange_other 6.117 r_scangle_it 4.751 r_scangle_other 4.749 r_mcangle_it 3.376 r_mcangle_other 3.376 r_scbond_it 3.228 r_scbond_other 3.226 r_mcbond_it 2.478 r_mcbond_other 2.474 r_angle_refined_deg 1.839 r_angle_other_deg 1.663 r_symmetry_xyhbond_nbd_other 0.244 r_symmetry_nbd_other 0.212 r_nbd_refined 0.205 r_nbd_other 0.193 r_xyhbond_nbd_refined 0.182 r_nbtor_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.146 r_symmetry_nbd_refined 0.131 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.083 r_gen_planes_refined 0.012 r_gen_planes_other 0.009 r_bond_refined_d r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1208 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing