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Crystal structure of Odorant Binding Protein 5 from Anopheles gambiae (AgamOBP5) with MPD (2-Methyl-2,4-pentanediol)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3Q8I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.12M Monosaccharides (0.02 M each of D-Glucose, D-Mannose, D-Galactose, L-Fucose, D-Xylose and N-Acetyl-D-Glucosamine), 0.1 M Bicine/Trizma base, pH 8.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350 and 12.5% (v/v) MPD (2-Methyl-2,4-pentanediol)
Crystal Properties Matthews coefficient Solvent content 2.31 46.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.943 α = 90 b = 35.509 β = 100.49 c = 55.063 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 PIXEL DECTRIS EIGER2 X 16M 2017-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.35 54.14 96.5 0.999 12.7 2.8 27461
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.42 95.9 0.749 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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.35 33.398 27448 1393 96.076 0.167 0.1657 0.1747 0.1941 0.1996 21.07
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] 0.772 0.383 0.138 -0.985
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.656 r_dihedral_angle_4_deg 22.11 r_dihedral_angle_3_deg 12.967 r_dihedral_angle_1_deg 6.108 r_lrange_it 5.974 r_lrange_other 5.885 r_scangle_it 5.063 r_scangle_other 5.06 r_scbond_it 3.323 r_scbond_other 3.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.656 r_dihedral_angle_4_deg 22.11 r_dihedral_angle_3_deg 12.967 r_dihedral_angle_1_deg 6.108 r_lrange_it 5.974 r_lrange_other 5.885 r_scangle_it 5.063 r_scangle_other 5.06 r_scbond_it 3.323 r_scbond_other 3.321 r_mcangle_it 2.594 r_mcangle_other 2.592 r_angle_refined_deg 1.89 r_mcbond_other 1.81 r_mcbond_it 1.809 r_angle_other_deg 1.563 r_symmetry_nbd_refined 0.293 r_nbd_refined 0.276 r_nbd_other 0.244 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.175 r_symmetry_xyhbond_nbd_refined 0.144 r_xyhbond_nbd_refined 0.136 r_metal_ion_refined 0.101 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 973 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing