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Crystal structure of a pheromone binding protein from Apis mellifera in complex with hexadecanoic acid
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 3.06 59.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.26 α = 90 b = 84.348 β = 90 c = 47.666 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 210 toroidal mirror 2007-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
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 58.72 99.1 0.062 0.062 15.2 5 11157 11157 32.73
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 2.11 99.5 0.459 0.459 3.8 5.1 1604
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 40 10190 10190 984 99.07 0.17609 0.17609 0.1726 0.186 0.21032 0.2186 RANDOM 41.526
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] 0.73 0.39 -1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.753 r_dihedral_angle_3_deg 15.837 r_dihedral_angle_4_deg 10.319 r_dihedral_angle_1_deg 6.14 r_scangle_it 2.265 r_scbond_it 1.546 r_angle_refined_deg 1.41 r_angle_other_deg 1.057 r_mcangle_it 0.952 r_mcbond_it 0.696
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.753 r_dihedral_angle_3_deg 15.837 r_dihedral_angle_4_deg 10.319 r_dihedral_angle_1_deg 6.14 r_scangle_it 2.265 r_scbond_it 1.546 r_angle_refined_deg 1.41 r_angle_other_deg 1.057 r_mcangle_it 0.952 r_mcbond_it 0.696 r_symmetry_vdw_other 0.248 r_xyhbond_nbd_refined 0.232 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.217 r_symmetry_hbond_refined 0.214 r_mcbond_other 0.197 r_nbd_other 0.182 r_nbtor_refined 0.179 r_chiral_restr 0.114 r_nbtor_other 0.093 r_bond_refined_d 0.013 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 899 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling REFMAC phasing