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Crystal structure of a pheromone binding protein from Apis mellifera with a serendipitous ligand at pH 5.5
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 1.7M ammonium sulfate, 0.1M sodium citrate, pH5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.1 60.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.879 α = 90 b = 84.21 β = 90 c = 46.831 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 4 Tiroidal mirror 2007-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 1.8 42.11 99.8 0.079 0.079 22.9 7.8 15535 15535 23.17
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 1.8 1.9 100 0.448 0.448 4.3 7.9 2231
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 1.8 30 14409 14409 1111 99.71 0.16112 0.16112 0.15871 0.1958 0.19289 0.2323 RANDOM 12.03
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] -0.05 0.41 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.569 r_dihedral_angle_3_deg 13.3 r_dihedral_angle_4_deg 9.052 r_dihedral_angle_1_deg 5.555 r_scangle_it 3.069 r_scbond_it 1.999 r_angle_other_deg 1.569 r_angle_refined_deg 1.365 r_mcangle_it 1.144 r_mcbond_it 0.646
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.569 r_dihedral_angle_3_deg 13.3 r_dihedral_angle_4_deg 9.052 r_dihedral_angle_1_deg 5.555 r_scangle_it 3.069 r_scbond_it 1.999 r_angle_other_deg 1.569 r_angle_refined_deg 1.365 r_mcangle_it 1.144 r_mcbond_it 0.646 r_mcbond_other 0.224 r_chiral_restr 0.089 r_bond_refined_d 0.014 r_bond_other_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 907 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 50
Software Software Software Name Purpose ADSC data collection REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing