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Crystal structure of Odorant Binding Protein 1 from Anopheles gambiae (AgamOBP1) with Icaridin (butan-2-yl 2-(2-hydroxyethyl)piperidine-1-carboxylate)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ERB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 32% PEG 8000, 250 mM MgCl2, 50 mM Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.15 42.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.984 α = 90 b = 68.476 β = 99.61 c = 61.675 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 CCD MARMOSAIC 225 mm CCD 1st mirror: Rh-coated Si mirror, bent for vertical collimation; 2nd mirror: Rh-coated toroidal Si mirror 2013-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1 MAX II I911-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.75 60.81 99.3 0.054 0.062 0.03 17.6 4.1 24664 24664
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.84 98.6 0.381 0.381 0.224 2 3.8 3531
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2ERB 1.75 60.81 23395 1253 99.17 0.1796 0.1775 0.1855 0.2209 0.2255 RANDOM 19.18
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] 0.6 -1.89 -0.28 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.751 r_dihedral_angle_3_deg 14.648 r_dihedral_angle_4_deg 12.057 r_dihedral_angle_1_deg 5.34 r_mcangle_it 1.43 r_angle_refined_deg 1.395 r_angle_other_deg 1.126 r_mcbond_it 0.862 r_mcbond_other 0.86 r_chiral_restr 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.751 r_dihedral_angle_3_deg 14.648 r_dihedral_angle_4_deg 12.057 r_dihedral_angle_1_deg 5.34 r_mcangle_it 1.43 r_angle_refined_deg 1.395 r_angle_other_deg 1.126 r_mcbond_it 0.862 r_mcbond_other 0.86 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2034 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 65
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing