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Structure of L289F 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 42.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.719 α = 90 b = 79.228 β = 111.027 c = 55.822 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 2021-02-03 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 1.56 50 100 0.101 0.04 0.906 32.1 7.2 51478
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 1.56 1.59 100 0.561 0.249 0.906 4 6
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 1.56 43.572 51478 2668 99.603 0.183 0.1817 0.1912 0.2006 0.2076 14.548
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 -0.008 0.012 -0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.338 r_dihedral_angle_4_deg 11.691 r_dihedral_angle_3_deg 11.491 r_dihedral_angle_1_deg 6.59 r_lrange_it 3.417 r_lrange_other 3.283 r_mcangle_it 1.362 r_mcangle_other 1.362 r_scangle_it 1.351 r_scangle_other 1.351
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.338 r_dihedral_angle_4_deg 11.691 r_dihedral_angle_3_deg 11.491 r_dihedral_angle_1_deg 6.59 r_lrange_it 3.417 r_lrange_other 3.283 r_mcangle_it 1.362 r_mcangle_other 1.362 r_scangle_it 1.351 r_scangle_other 1.351 r_angle_other_deg 1.19 r_angle_refined_deg 1.16 r_scbond_it 0.807 r_scbond_other 0.807 r_mcbond_it 0.75 r_mcbond_other 0.749 r_nbd_refined 0.195 r_symmetry_nbd_refined 0.176 r_symmetry_nbd_other 0.163 r_nbtor_refined 0.159 r_symmetry_metal_ion_refined 0.118 r_xyhbond_nbd_refined 0.116 r_nbd_other 0.115 r_metal_ion_refined 0.113 r_symmetry_xyhbond_nbd_refined 0.08 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.054 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 2597 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing