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Crystal structure of Odorant Binding Protein 5 from Anopheles gambiae (AgamOBP5) with Carvacrol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BXU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.12M alcohols (0.02 M each of 1,6-Hexanediol, 1-Butanol, 1,2-Propanediol (racemic), 2-Propanol, 1,4- Butanediol and 1,3-Propanediol), 0.1 M MOPS/HEPES-Na pH 7.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD
Crystal Properties Matthews coefficient Solvent content 2.39 48.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.361 α = 90 b = 36.71 β = 101.771 c = 54.658 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 XE 9M 2019-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
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 1.3 53.51 97.5 0.999 23.5 6.4 32113
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 1.3 1.37 96.3 0.985 7.5 5.7
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 1.3 26.769 32094 1602 97.193 0.173 0.1718 0.1811 0.2009 0.2021 21.714
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] -0.028 0.242 1.085 -1.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.144 r_dihedral_angle_4_deg 24.114 r_dihedral_angle_3_deg 13.95 r_dihedral_angle_1_deg 5.777 r_lrange_it 5.171 r_lrange_other 5.048 r_scangle_it 3.944 r_scangle_other 3.941 r_scbond_it 2.676 r_scbond_other 2.674
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.144 r_dihedral_angle_4_deg 24.114 r_dihedral_angle_3_deg 13.95 r_dihedral_angle_1_deg 5.777 r_lrange_it 5.171 r_lrange_other 5.048 r_scangle_it 3.944 r_scangle_other 3.941 r_scbond_it 2.676 r_scbond_other 2.674 r_mcangle_it 2.126 r_mcangle_other 2.126 r_angle_refined_deg 1.83 r_mcbond_it 1.603 r_mcbond_other 1.601 r_angle_other_deg 1.551 r_nbd_refined 0.225 r_nbd_other 0.205 r_nbtor_refined 0.176 r_symmetry_nbd_other 0.173 r_symmetry_nbd_refined 0.133 r_symmetry_xyhbond_nbd_refined 0.118 r_xyhbond_nbd_refined 0.113 r_chiral_restr 0.094 r_symmetry_nbtor_other 0.082 r_bond_refined_d 0.015 r_chiral_restr_other 0.011 r_gen_planes_refined 0.009 r_metal_ion_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 973 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing