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Crystal structure of a pheromone binding protein from Apis mellifera in complex with the 9-keto-2(E)-decenoic 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 2.97 58.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.099 α = 90 b = 84.281 β = 90 c = 47.602 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 315r cylindrical grazing incidence mirror 2007-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.979 ESRF ID29
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 2.15 57.3 100 0.072 0.072 16.6 6.9 9124 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 2.15 2.27 100 0.492 0.492 3.8 7.2 1273
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 2.15 40 7975 7975 882 99.93 0.20848 0.20848 0.20353 0.2131 0.25223 0.2688 RANDOM 40.979
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] 1.69 -0.13 -1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.565 r_dihedral_angle_4_deg 18.712 r_dihedral_angle_3_deg 14.917 r_dihedral_angle_1_deg 5.384 r_scangle_it 1.583 r_angle_refined_deg 1.279 r_scbond_it 1.187 r_angle_other_deg 0.962 r_mcangle_it 0.72 r_mcbond_it 0.641
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.565 r_dihedral_angle_4_deg 18.712 r_dihedral_angle_3_deg 14.917 r_dihedral_angle_1_deg 5.384 r_scangle_it 1.583 r_angle_refined_deg 1.279 r_scbond_it 1.187 r_angle_other_deg 0.962 r_mcangle_it 0.72 r_mcbond_it 0.641 r_symmetry_hbond_refined 0.38 r_symmetry_vdw_other 0.228 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.2 r_nbd_other 0.194 r_nbtor_refined 0.177 r_symmetry_vdw_refined 0.153 r_mcbond_other 0.128 r_nbtor_other 0.089 r_chiral_restr 0.074 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 907 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling REFMAC phasing