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Crystal structure of juvenile hormone acid methyltransferase silkworm JHAMT isoform3 complex with S-Adenosyl-L-homocysteine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7V2S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 0.15M DL-malic acid pH 7.0, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.35 47.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.15 α = 90 b = 69.17 β = 99.98 c = 57.82 γ = 90
Symmetry Space Group C 1 2 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 2018-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.9792 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.53 56.956 96.6 0.083 0.096 11.9 6.9 18812
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.53 2.6 0.856 0.524 2
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 7V2S 2.53 56.956 18811 904 96.314 0.195 0.192 0.1933 0.2414 0.2404 74.103
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] -0.015 -0.041 0.053
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.277 r_dihedral_angle_3_deg 18.134 r_lrange_it 12.817 r_lrange_other 12.816 r_dihedral_angle_4_deg 12.492 r_scangle_it 10.123 r_scangle_other 10.121 r_mcangle_other 7.798 r_mcangle_it 7.797 r_dihedral_angle_1_deg 7.575
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.277 r_dihedral_angle_3_deg 18.134 r_lrange_it 12.817 r_lrange_other 12.816 r_dihedral_angle_4_deg 12.492 r_scangle_it 10.123 r_scangle_other 10.121 r_mcangle_other 7.798 r_mcangle_it 7.797 r_dihedral_angle_1_deg 7.575 r_scbond_it 6.661 r_scbond_other 6.66 r_mcbond_it 5.401 r_mcbond_other 5.387 r_angle_other_deg 2.261 r_angle_refined_deg 1.492 r_nbd_other 0.255 r_symmetry_xyhbond_nbd_refined 0.235 r_symmetry_nbd_other 0.221 r_nbd_refined 0.202 r_symmetry_nbd_refined 0.193 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.156 r_symmetry_nbtor_other 0.069 r_chiral_restr 0.065 r_bond_other_d 0.034 r_gen_planes_other 0.007 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_symmetry_xyhbond_nbd_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4188 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing