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Structure of Hyoscyamine 6-beta Hydroxylase in complex with iron, succinate, and 6-OH-hyoscyamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TTM 6TTM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG 3350, sodium formate, strontium chloride
Crystal Properties Matthews coefficient Solvent content 2.16 42.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.839 α = 90 b = 79.258 β = 111.22 c = 55.96 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 PIXEL DECTRIS PILATUS3 6M 2021-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03317 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.58 50 98.6 0.086 0.036 0.997 20.1 6.3 48707
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.58 1.61 98.7 0.675 0.364 0.697 2.3 4.1
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 6TTM 1.581 43.613 48707 2534 97.635 0.186 0.1853 0.1955 0.2055 0.2146 14.871
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] -0.004 0.005 -0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.319 r_dihedral_angle_4_deg 13.518 r_dihedral_angle_3_deg 11.896 r_dihedral_angle_1_deg 6.489 r_lrange_it 3.421 r_lrange_other 3.254 r_scangle_it 1.48 r_scangle_other 1.479 r_mcangle_it 1.344 r_mcangle_other 1.343
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.319 r_dihedral_angle_4_deg 13.518 r_dihedral_angle_3_deg 11.896 r_dihedral_angle_1_deg 6.489 r_lrange_it 3.421 r_lrange_other 3.254 r_scangle_it 1.48 r_scangle_other 1.479 r_mcangle_it 1.344 r_mcangle_other 1.343 r_angle_other_deg 1.197 r_angle_refined_deg 1.17 r_scbond_it 0.899 r_scbond_other 0.898 r_mcbond_it 0.749 r_mcbond_other 0.749 r_nbd_refined 0.198 r_symmetry_nbd_refined 0.19 r_symmetry_nbd_other 0.162 r_nbtor_refined 0.16 r_xyhbond_nbd_refined 0.131 r_symmetry_metal_ion_refined 0.13 r_nbd_other 0.122 r_symmetry_xyhbond_nbd_refined 0.099 r_metal_ion_refined 0.086 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.056 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2578 Nucleic Acid Atoms Solvent Atoms 265 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing