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Structure of Hyoscyamine 6-beta Hydroxylase in complex with iron, 2-oxoglutarate, 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 2.15 42.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.801 α = 90 b = 79.329 β = 110.994 c = 55.848 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 CCD RAYONIX MX-300 2020-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.53 50 99.9 0.046 0.018 0.93 34.8 7.6 54702
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 1.53 1.56 99 0.371 0.157 0.93 5 6.5
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 1.532 43.61 54702 2694 99.914 0.184 0.1826 0.1916 0.2037 0.2116 14.553
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] 0.001 -0.001 0.003 -0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.5 r_dihedral_angle_4_deg 12.667 r_dihedral_angle_3_deg 12.033 r_dihedral_angle_1_deg 6.59 r_lrange_it 4.17 r_lrange_other 3.937 r_scangle_it 1.372 r_scangle_other 1.372 r_mcangle_it 1.273 r_mcangle_other 1.272
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.5 r_dihedral_angle_4_deg 12.667 r_dihedral_angle_3_deg 12.033 r_dihedral_angle_1_deg 6.59 r_lrange_it 4.17 r_lrange_other 3.937 r_scangle_it 1.372 r_scangle_other 1.372 r_mcangle_it 1.273 r_mcangle_other 1.272 r_angle_other_deg 1.201 r_angle_refined_deg 1.15 r_scbond_it 0.836 r_scbond_other 0.836 r_mcbond_it 0.706 r_mcbond_other 0.705 r_symmetry_nbd_refined 0.222 r_symmetry_xyhbond_nbd_refined 0.199 r_nbd_refined 0.196 r_nbtor_refined 0.161 r_symmetry_nbd_other 0.16 r_nbd_other 0.124 r_xyhbond_nbd_refined 0.117 r_metal_ion_refined 0.076 r_symmetry_nbtor_other 0.074 r_symmetry_metal_ion_refined 0.074 r_chiral_restr 0.055 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 311 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing