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Crystal structure of a pheromone binding protein from Apis mellifera with a serendipitous ligand soaked at pH 7.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H8V PDB ENTRY 2H8V
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 60.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.298 α = 90 b = 83.909 β = 90 c = 46.804 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 1.75 41.96 99.9 0.087 0.087 21.2 7.9 16926 16926 21.99
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 1.75 1.84 100 0.484 0.484 4.1 8 2441
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 2H8V 1.75 30 15916 15916 992 99.89 0.16238 0.16238 0.16084 0.2038 0.18689 0.2314 RANDOM 11.954
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] 0.06 0.09 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.404 r_dihedral_angle_3_deg 12.752 r_dihedral_angle_4_deg 11.02 r_dihedral_angle_1_deg 5.404 r_scangle_it 2.839 r_scbond_it 1.835 r_angle_refined_deg 1.277 r_angle_other_deg 1.208 r_mcangle_it 1.141 r_mcbond_it 0.632
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.404 r_dihedral_angle_3_deg 12.752 r_dihedral_angle_4_deg 11.02 r_dihedral_angle_1_deg 5.404 r_scangle_it 2.839 r_scbond_it 1.835 r_angle_refined_deg 1.277 r_angle_other_deg 1.208 r_mcangle_it 1.141 r_mcbond_it 0.632 r_mcbond_other 0.194 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 907 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 44
Software Software Software Name Purpose ADSC data collection REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing