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Structure of Anopheles gambiae OBP9 in complex with Methyl eugenol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 29LI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.12 M Ethylene glycols:
0.3M Diethylene glycol; 0.3M Triethylene
glycol; 0.3M Tetraethylene glycol; 0.3M
Pentaethylene glycol
0.1 M Imidazole; MES monohydrate (acid)
pH 6.5
30% v/v Mix 1:
40% v/v PEG 500* MME; 20% w/v PEG 20000
Crystal Properties Matthews coefficient Solvent content 1.73 28.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.686 α = 90 b = 43.961 β = 90 c = 62.025 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 EIGER X 16M 2022-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.88559 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.2 62.03 99.4 0.073 0.076 0.022 0.997 26.4 13 31058
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 1.2 1.22 99.8 0.147 0.152 0.04 0.995 13.5
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 1.2 35.87 29494 1509 99.28 0.15508 0.15361 0.1612 0.18167 0.1886 RANDOM 13.667
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] 0.77 -0.17 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.733 r_long_range_B_refined 11.509 r_long_range_B_other 11.28 r_dihedral_angle_2_deg 9.618 r_scangle_other 7.416 r_mcangle_it 5.771 r_mcangle_other 5.771 r_dihedral_angle_1_deg 5.565 r_scbond_it 5.095 r_scbond_other 5.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.733 r_long_range_B_refined 11.509 r_long_range_B_other 11.28 r_dihedral_angle_2_deg 9.618 r_scangle_other 7.416 r_mcangle_it 5.771 r_mcangle_other 5.771 r_dihedral_angle_1_deg 5.565 r_scbond_it 5.095 r_scbond_other 5.092 r_mcbond_it 3.998 r_mcbond_other 3.973 r_rigid_bond_restr 3.748 r_angle_refined_deg 2.076 r_angle_other_deg 0.772 r_chiral_restr 0.11 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 978 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing PDB_EXTRACT data extraction