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Crystal structure of a pheromone binding protein from Apis mellifera in complex with the Queen mandibular pheromone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R5R PDB ENTRY 1R5R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 1.8M ammonium sulphate, 0.1M sodium citrate, pH5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.02 59.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.461 α = 90 b = 85.019 β = 90 c = 48.345 γ = 90
Symmetry Space Group C 2 2 21
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 ADSC QUANTUM 4r Tiroidal mirror 2007-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.25 57.3 100 0.067 0.067 16.9 4.5 7888 7888 43.67
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.37 99.9 0.518 0.518 2.7 4.4 1119
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1R5R 2.25 40 7107 7107 769 99.95 0.18598 0.18598 0.18059 0.1879 0.23581 0.2396 RANDOM 55.524
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] 1.05 -0.65 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.645 r_dihedral_angle_3_deg 14.69 r_dihedral_angle_4_deg 10.36 r_dihedral_angle_1_deg 5.406 r_scangle_it 1.905 r_scbond_it 1.385 r_angle_refined_deg 1.278 r_angle_other_deg 0.915 r_mcangle_it 0.787 r_mcbond_it 0.633
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.645 r_dihedral_angle_3_deg 14.69 r_dihedral_angle_4_deg 10.36 r_dihedral_angle_1_deg 5.406 r_scangle_it 1.905 r_scbond_it 1.385 r_angle_refined_deg 1.278 r_angle_other_deg 0.915 r_mcangle_it 0.787 r_mcbond_it 0.633 r_symmetry_vdw_refined 0.252 r_nbd_refined 0.225 r_symmetry_vdw_other 0.202 r_nbd_other 0.188 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.176 r_symmetry_hbond_refined 0.173 r_mcbond_other 0.134 r_nbtor_other 0.089 r_chiral_restr 0.07 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 907 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling REFMAC phasing