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Dimeric crystal structure of a pheromone binding protein from Apis mellifera in complex with the n-butyl benzene sulfonamide at pH 7.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CYZ PDB ENTRY 3CYZ
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 2.06 40.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.56 α = 90 b = 75.167 β = 90 c = 83.798 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 Q4R 188 Tiroidal mirror 2006-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3
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 1.7 37.58 99.5 0.082 0.082 19.4 5.9 24649 24649 17.49
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 1.7 1.79 99.2 0.344 0.344 4 6 3512
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 3CYZ 1.7 30 23357 23357 1256 99.36 0.1528 0.1528 0.15077 0.1635 0.19191 0.2007 RANDOM 17.08
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] 1.72 -1.24 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.137 r_dihedral_angle_3_deg 12.432 r_dihedral_angle_4_deg 12.274 r_dihedral_angle_1_deg 5.363 r_scangle_it 2.732 r_scbond_it 2.03 r_angle_refined_deg 1.391 r_angle_other_deg 1.114 r_mcangle_it 1.095 r_mcbond_it 1.021
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.137 r_dihedral_angle_3_deg 12.432 r_dihedral_angle_4_deg 12.274 r_dihedral_angle_1_deg 5.363 r_scangle_it 2.732 r_scbond_it 2.03 r_angle_refined_deg 1.391 r_angle_other_deg 1.114 r_mcangle_it 1.095 r_mcbond_it 1.021 r_symmetry_vdw_refined 0.247 r_nbd_refined 0.223 r_symmetry_vdw_other 0.218 r_mcbond_other 0.211 r_nbd_other 0.191 r_nbtor_refined 0.181 r_symmetry_hbond_refined 0.172 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.152 r_nbtor_other 0.089 r_bond_refined_d 0.013 r_bond_other_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1813 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling REFMAC phasing