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Crystal structure of Odorant Binding Protein 5 from Anopheles gambiae (AgamOBP5) with Thymol
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 7.5 293 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 2.4 48.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.241 α = 90 b = 36.566 β = 100.383 c = 54.962 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 54.06 94.3 0.999 22.5 6.4 31153
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 97.8 0.98 6.7
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 54.06 31140 1581 93.948 0.187 0.1851 0.1942 0.2202 0.2281 22.994
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] -0.221 0.265 0.89 -0.719
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.476 r_dihedral_angle_4_deg 16.419 r_dihedral_angle_3_deg 14.105 r_dihedral_angle_1_deg 6.396 r_lrange_it 6.097 r_lrange_other 6.006 r_scangle_it 4.349 r_scangle_other 4.347 r_scbond_it 2.996 r_scbond_other 2.994
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.476 r_dihedral_angle_4_deg 16.419 r_dihedral_angle_3_deg 14.105 r_dihedral_angle_1_deg 6.396 r_lrange_it 6.097 r_lrange_other 6.006 r_scangle_it 4.349 r_scangle_other 4.347 r_scbond_it 2.996 r_scbond_other 2.994 r_mcangle_it 2.601 r_mcangle_other 2.6 r_angle_refined_deg 1.958 r_mcbond_other 1.807 r_mcbond_it 1.803 r_angle_other_deg 1.541 r_nbd_refined 0.295 r_nbd_other 0.2 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.155 r_symmetry_xyhbond_nbd_refined 0.121 r_metal_ion_refined 0.12 r_symmetry_nbd_refined 0.108 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.089 r_bond_refined_d 0.015 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 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling REFMAC phasing