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Dimeric crystal structure of a pheromone binding protein from Apis mellifera in complex with 9-keto-2(E)-decenoic acid at pH 7.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BJH PDB ENTRY 3BJH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.2M magnesium chloride, 0.1M Tris, 15% PEG8000, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.285 α = 90 b = 75.555 β = 90 c = 84.113 γ = 90
Symmetry Space Group P 21 21 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 315 cylindrical gazing 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 1.8 84.25 96.4 0.091 0.091 16.9 6.9 21263 21263 17.97
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 84.1 0.457 0.457 3.7 6.9 2614
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3BJH 1.8 20 20184 20184 1057 96.03 0.16372 0.16372 0.16181 0.176 0.19964 0.2098 RANDOM 16.682
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] 2.1 -1.69 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.804 r_dihedral_angle_3_deg 14 r_dihedral_angle_4_deg 10.937 r_dihedral_angle_1_deg 4.836 r_scangle_it 2.654 r_scbond_it 1.835 r_angle_refined_deg 1.413 r_angle_other_deg 1.028 r_mcangle_it 0.965 r_mcbond_it 0.799
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.804 r_dihedral_angle_3_deg 14 r_dihedral_angle_4_deg 10.937 r_dihedral_angle_1_deg 4.836 r_scangle_it 2.654 r_scbond_it 1.835 r_angle_refined_deg 1.413 r_angle_other_deg 1.028 r_mcangle_it 0.965 r_mcbond_it 0.799 r_nbd_refined 0.239 r_mcbond_other 0.209 r_nbd_other 0.204 r_symmetry_vdw_other 0.202 r_symmetry_vdw_refined 0.195 r_xyhbond_nbd_refined 0.194 r_nbtor_refined 0.18 r_symmetry_hbond_refined 0.16 r_nbtor_other 0.091 r_chiral_restr 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_bond_other_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1784 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling AMoRE phasing