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Structure of Anopheles gambiae OBP9 in complex with PMD (P-Menthane-3,8-diol)
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 1.71 28.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.341 α = 90 b = 43.959 β = 90 c = 62.055 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 62.05 99.2 0.07 0.073 0.02 0.998 17.5 13 30763
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 1.22 100 0.402 0.418 0.112 0.985 13.4
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 1.2 35.87 29198 1492 99.18 0.1689 0.16725 0.1743 0.19859 0.2057 RANDOM 19.785
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] 2.1 0.16 -2.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.392 r_long_range_B_refined 12.612 r_long_range_B_other 12.423 r_scangle_other 9.212 r_mcangle_other 7.157 r_mcangle_it 7.15 r_scbond_it 6.477 r_scbond_other 6.473 r_dihedral_angle_2_deg 5.687 r_mcbond_it 5.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.392 r_long_range_B_refined 12.612 r_long_range_B_other 12.423 r_scangle_other 9.212 r_mcangle_other 7.157 r_mcangle_it 7.15 r_scbond_it 6.477 r_scbond_other 6.473 r_dihedral_angle_2_deg 5.687 r_mcbond_it 5.082 r_mcbond_other 5.052 r_dihedral_angle_1_deg 4.999 r_rigid_bond_restr 3.477 r_angle_refined_deg 1.972 r_angle_other_deg 0.961 r_chiral_restr 0.198 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.003 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 961 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing PDB_EXTRACT data extraction