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Crystal structure of juvenile hormone acid methyltransferase CfJHAMT in complex with SAH and juvenile hormone III acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9XYQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 296 0.1 M magnesium formate and 15% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.01 38.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.923 α = 90 b = 40.744 β = 90.75 c = 96.761 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 PILATUS3 S 6M 2022-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.77 40.74 96 0.04 0.049 0.027 0.999 13.4 3 25705
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.87 96.7 0.531 0.648 0.365 0.805 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.77 37.58 24440 1258 95.76 0.1847 0.18233 0.1898 0.23252 0.2429 RANDOM 37.273
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] -1.11 -0.27 -1.73 2.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.335 r_dihedral_angle_4_deg 22.989 r_dihedral_angle_3_deg 17.141 r_long_range_B_refined 6.94 r_long_range_B_other 6.932 r_dihedral_angle_1_deg 6.732 r_scangle_other 5.285 r_scbond_it 3.398 r_scbond_other 3.396 r_mcangle_it 3.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.335 r_dihedral_angle_4_deg 22.989 r_dihedral_angle_3_deg 17.141 r_long_range_B_refined 6.94 r_long_range_B_other 6.932 r_dihedral_angle_1_deg 6.732 r_scangle_other 5.285 r_scbond_it 3.398 r_scbond_other 3.396 r_mcangle_it 3.323 r_mcangle_other 3.322 r_mcbond_it 2.382 r_mcbond_other 2.382 r_angle_refined_deg 1.855 r_angle_other_deg 1.447 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2189 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement SCALA data scaling XDS data reduction MOLREP phasing