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X-ray structure of Canis familiaris Odorant Binding Protein 2 bound to citronellal
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L4R 3L4R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 35% PEG 4000, 0.2 M MgCl2 in 0.1 M pH 8.0 Tris buffer
Crystal Properties Matthews coefficient Solvent content 2.03 39.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.562 α = 90 b = 48.685 β = 105.197 c = 67.102 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 EIGER X 16M 2020-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.978566 SOLEIL PROXIMA 1
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 1.74 48.69 97 0.052 0.056 0.021 0.999 19 6.9 32275 24.03
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 1.74 1.77 85 0.376 0.407 0.153 0.949 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3L4R 1.74 38.91 1.34 32251 1575 96.62 0.1918 0.1903 0.1914 0.2189 0.2194 29.9
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.7597 f_angle_d 0.807 f_chiral_restr 0.0556 f_bond_d 0.0059 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2422 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 24
Software Software Software Name Purpose PHENIX refinement Aimless data scaling MOLREP phasing