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Structure of L289F Hyoscyamine 6-beta Hydroxylase in complex with iron, 2-oxoglutarate, and 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 42.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.763 α = 90 b = 79.215 β = 111.053 c = 55.757 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 EIGER X 16M 2020-10-16 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 1.53 50 96.6 0.089 0.04 0.995 22.1 5.5 52325
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 89.4 0.451 0.238 0.863 4.2 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 1.53 43.529 52325 2572 95.578 0.185 0.1845 0.1947 0.2043 0.2137 14.197
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 0.002 -0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.276 r_dihedral_angle_4_deg 12.547 r_dihedral_angle_3_deg 11.584 r_dihedral_angle_1_deg 6.567 r_lrange_it 3.83 r_lrange_other 3.501 r_scangle_it 1.265 r_scangle_other 1.265 r_angle_refined_deg 1.2 r_mcangle_it 1.191
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.276 r_dihedral_angle_4_deg 12.547 r_dihedral_angle_3_deg 11.584 r_dihedral_angle_1_deg 6.567 r_lrange_it 3.83 r_lrange_other 3.501 r_scangle_it 1.265 r_scangle_other 1.265 r_angle_refined_deg 1.2 r_mcangle_it 1.191 r_mcangle_other 1.19 r_angle_other_deg 1.189 r_scbond_other 0.778 r_scbond_it 0.777 r_mcbond_it 0.66 r_mcbond_other 0.66 r_nbd_refined 0.194 r_symmetry_nbd_refined 0.179 r_symmetry_xyhbond_nbd_refined 0.179 r_symmetry_nbd_other 0.163 r_nbtor_refined 0.16 r_nbd_other 0.121 r_xyhbond_nbd_refined 0.115 r_metal_ion_refined 0.111 r_symmetry_metal_ion_refined 0.103 r_symmetry_nbtor_other 0.075 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 2572 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing