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Structure of L289F Hyoscyamine 6-beta Hydroxylase in complex with vanadyl, succinate, 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 2.16 43.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.783 α = 90 b = 79.901 β = 111.244 c = 55.675 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 97 0.123 0.053 0.994 26.4 5.6 52983
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 92.6 0.468 0.278 0.839 3.4 3.4
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 43.557 52983 2526 96.549 0.182 0.1809 0.1921 0.2011 0.2096 14.504
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] -0.003 -0.007 0.01 -0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.249 r_dihedral_angle_4_deg 13.464 r_dihedral_angle_3_deg 12.82 r_dihedral_angle_1_deg 6.724 r_lrange_it 3.771 r_lrange_other 3.546 r_scangle_it 1.514 r_scangle_other 1.514 r_mcangle_it 1.284 r_mcangle_other 1.283
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.249 r_dihedral_angle_4_deg 13.464 r_dihedral_angle_3_deg 12.82 r_dihedral_angle_1_deg 6.724 r_lrange_it 3.771 r_lrange_other 3.546 r_scangle_it 1.514 r_scangle_other 1.514 r_mcangle_it 1.284 r_mcangle_other 1.283 r_angle_other_deg 1.276 r_angle_refined_deg 1.268 r_scbond_it 0.931 r_scbond_other 0.929 r_mcbond_it 0.725 r_mcbond_other 0.725 r_symmetry_nbd_refined 0.355 r_nbd_other 0.242 r_nbd_refined 0.205 r_symmetry_nbd_other 0.167 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.164 r_symmetry_xyhbond_nbd_refined 0.143 r_metal_ion_refined 0.126 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.064 r_symmetry_metal_ion_refined 0.043 r_symmetry_xyhbond_nbd_other 0.019 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 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 364 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing