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Juvenile hormone binding protein complexed with 2-Methyl-1-(4-butylbenzyl)-benzimidazole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AOS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M sodium acetate (pH 5.6), 1.7M ammonium sulfate, 3% (v/v) 1,6-hexanediol
Crystal Properties Matthews coefficient Solvent content 3.06 59.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.074 α = 90 b = 88.074 β = 90 c = 135.48 γ = 120
Symmetry Space Group P 63 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS PILATUS 2M 2020-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.4 100 100 0.178 0.029 0.999 19.3 36.9 12778
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 2.063 0.333 0.866 2.3
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.4 38.89 12715 661 99.616 0.238 0.2355 0.2411 0.285 0.2866 RANDOM 58.475
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] -1.478 -0.739 -1.478 4.795
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.308 r_dihedral_angle_6_deg 12.512 r_lrange_it 6.887 r_lrange_other 6.866 r_dihedral_angle_2_deg 6.793 r_dihedral_angle_1_deg 5.887 r_scangle_it 4.382 r_scangle_other 4.38 r_mcangle_other 4.137 r_mcangle_it 4.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.308 r_dihedral_angle_6_deg 12.512 r_lrange_it 6.887 r_lrange_other 6.866 r_dihedral_angle_2_deg 6.793 r_dihedral_angle_1_deg 5.887 r_scangle_it 4.382 r_scangle_other 4.38 r_mcangle_other 4.137 r_mcangle_it 4.135 r_scbond_it 2.58 r_scbond_other 2.578 r_mcbond_it 2.485 r_mcbond_other 2.469 r_angle_refined_deg 0.948 r_angle_other_deg 0.355 r_symmetry_nbd_refined 0.21 r_symmetry_nbd_other 0.197 r_nbd_refined 0.193 r_nbtor_refined 0.169 r_nbd_other 0.139 r_xyhbond_nbd_refined 0.132 r_symmetry_nbtor_other 0.079 r_symmetry_xyhbond_nbd_refined 0.079 r_chiral_restr 0.049 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1693 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement XDS data reduction pointless data scaling MOLREP phasing