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Crystal structure of juvenile hormone acid methyltransferase castaneum JHAMT3 from Tribolium castaneum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7EBS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 289 0.1 M Bis-Tris pH 5.5, 0.2 M Sodium chloride, and 25% polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.269 45.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.597 α = 90 b = 71.476 β = 90 c = 133.984 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M 2023-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97918 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.5 48.88 99.2 0.17 0.18 0.057 9.1 9.2 19950
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 99.8 0.927 0.977 0.301 2.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.5 48.88 19900 974 98.848 0.247 0.2449 0.2452 0.2945 0.2952 36.047
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] -1.562 2.843 -1.281
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.969 r_dihedral_angle_4_deg 20.403 r_dihedral_angle_3_deg 16.544 r_lrange_it 7.548 r_lrange_other 7.548 r_dihedral_angle_1_deg 7.515 r_scangle_it 5.595 r_scangle_other 5.595 r_mcangle_it 4.198 r_mcangle_other 4.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.969 r_dihedral_angle_4_deg 20.403 r_dihedral_angle_3_deg 16.544 r_lrange_it 7.548 r_lrange_other 7.548 r_dihedral_angle_1_deg 7.515 r_scangle_it 5.595 r_scangle_other 5.595 r_mcangle_it 4.198 r_mcangle_other 4.198 r_scbond_it 3.371 r_scbond_other 3.37 r_mcbond_it 2.623 r_mcbond_other 2.621 r_angle_other_deg 2.245 r_angle_refined_deg 1.523 r_symmetry_xyhbond_nbd_refined 0.403 r_symmetry_nbd_refined 0.379 r_nbd_other 0.341 r_symmetry_nbd_other 0.226 r_nbd_refined 0.199 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.148 r_symmetry_xyhbond_nbd_other 0.103 r_chiral_restr 0.072 r_symmetry_nbtor_other 0.071 r_bond_other_d 0.034 r_gen_planes_other 0.008 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4301 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction PROCOR data scaling MOLREP phasing