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Crystal structure of juvenile hormone acid methyltransferase JHAMT from Choristoneura fumiferana (CfJHAMT) in complex with SAH (crystal form 1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CCF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 296 0.1 M Magnesium formate, 15 %(w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.08 40.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.925 α = 90 b = 39.224 β = 97.95 c = 104.674 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 2020-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 1.6039 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 2.1 39.22 95.8 0.053 0.067 0.026 0.999 15.3 6.6 15890
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 2.1 2.21 93.5 0.768 0.912 0.351 0.842 6.4
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 2.1 36.71 15142 739 95.12 0.21036 0.20819 0.2139 0.25353 0.2544 RANDOM 68.065
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] -1.44 0.28 -2.97 4.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.269 r_dihedral_angle_3_deg 20.853 r_dihedral_angle_4_deg 19.091 r_long_range_B_other 7.688 r_long_range_B_refined 7.687 r_dihedral_angle_1_deg 6.919 r_scangle_other 5.508 r_mcangle_it 3.915 r_mcangle_other 3.913 r_scbond_it 3.417
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.269 r_dihedral_angle_3_deg 20.853 r_dihedral_angle_4_deg 19.091 r_long_range_B_other 7.688 r_long_range_B_refined 7.687 r_dihedral_angle_1_deg 6.919 r_scangle_other 5.508 r_mcangle_it 3.915 r_mcangle_other 3.913 r_scbond_it 3.417 r_scbond_other 3.415 r_mcbond_it 2.732 r_mcbond_other 2.629 r_angle_refined_deg 1.852 r_angle_other_deg 1.448 r_chiral_restr 0.08 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 1615 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement SCALA data scaling XDS data reduction BALBES phasing