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Crystal structure of juvenile hormone acid methyltransferase CfJHAMT in complex with SAH (crystal form 2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9XYO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8.5 296 0.2 M Calcium chloride, 0.1 M TRIS pH 8.5, 25 %(w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.11 41.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.471 α = 90.02 b = 193.835 β = 90.13 c = 34.788 γ = 89.98
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 2021-07-21 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 2.84 48.46 90 0.072 0.102 0.072 0.993 4.7 1.9 22456
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 2.84 2.99 0.263 0.372 0.263 0.874 2
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 2.84 48.46 21313 1142 89.51 0.18127 0.17945 0.1823 0.21473 0.2152 RANDOM 41.576
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] -42.15 -1.25 -4.85 42.12 -9.91 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.827 r_dihedral_angle_3_deg 21.516 r_dihedral_angle_4_deg 16.384 r_long_range_B_refined 13.962 r_long_range_B_other 13.962 r_mcangle_it 7.339 r_mcangle_other 7.339 r_dihedral_angle_1_deg 7.251 r_scangle_other 6.258 r_mcbond_it 4.706
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.827 r_dihedral_angle_3_deg 21.516 r_dihedral_angle_4_deg 16.384 r_long_range_B_refined 13.962 r_long_range_B_other 13.962 r_mcangle_it 7.339 r_mcangle_other 7.339 r_dihedral_angle_1_deg 7.251 r_scangle_other 6.258 r_mcbond_it 4.706 r_mcbond_other 4.706 r_scbond_it 3.959 r_scbond_other 3.959 r_angle_refined_deg 1.763 r_angle_other_deg 1.316 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 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 8177 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing