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Structure of Anopheles gambiae OBP9 in complex with n-Butyl cinnamate
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 0.06 M Divalents :
0.3M Magnesium chloride hexahydrate;
0.3M Calcium chloride dihydrate
0.1 M Imidazole; MES monohydrate (acid)
pH 6.5
37.5% v/v Mix 4:
25% v/v MPD; 25% PEG
1000; 25% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.66 25.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.223 α = 90 b = 45.182 β = 90 c = 64.178 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 2022-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9762 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 45.18 100 0.109 0.113 0.032 0.995 15.4 12.5 30092
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 1.26 100 0.235 0.245 0.069 0.98 12.2
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 1.2 36.94 28521 1507 99.95 0.1376 0.13662 0.1436 0.15597 0.1595 RANDOM 13.14
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] 0.04 0.14 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.504 r_long_range_B_refined 12.43 r_long_range_B_other 11.838 r_dihedral_angle_2_deg 8.797 r_scangle_other 8.279 r_mcangle_other 5.823 r_mcangle_it 5.817 r_scbond_it 5.752 r_scbond_other 5.748 r_dihedral_angle_1_deg 5.601
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.504 r_long_range_B_refined 12.43 r_long_range_B_other 11.838 r_dihedral_angle_2_deg 8.797 r_scangle_other 8.279 r_mcangle_other 5.823 r_mcangle_it 5.817 r_scbond_it 5.752 r_scbond_other 5.748 r_dihedral_angle_1_deg 5.601 r_mcbond_it 4.016 r_mcbond_other 3.977 r_rigid_bond_restr 3.886 r_angle_refined_deg 1.508 r_angle_other_deg 0.601 r_chiral_restr 0.362 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 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 99 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement SCALA data scaling MOLREP phasing PDB_EXTRACT data extraction XDS data reduction