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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 6.9 293 0.2M magnesium chloride, 0.1M Tris, 15% PEG8000, pH6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.13 42.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.413 α = 90 b = 75.652 β = 90 c = 84.101 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 Tiroidal mirror 2006-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.954 ESRF ID23-1
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 1.5 56.25 99.4 0.078 0.078 12.7 3.9 36737 36737 14.21
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 1.5 1.58 100 0.301 0.301 3.7 3.9 5313
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 1.5 20 35532 35532 1144 99.13 0.15331 0.15331 0.1518 0.164 0.19844 0.2029 RANDOM 12.421
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] 1.07 -0.76 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.224 r_dihedral_angle_4_deg 12.88 r_dihedral_angle_3_deg 12.722 r_sphericity_free 6.08 r_dihedral_angle_1_deg 5.046 r_scangle_it 3.479 r_scbond_it 2.628 r_sphericity_bonded 2.407 r_mcangle_it 1.819 r_angle_refined_deg 1.601
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.224 r_dihedral_angle_4_deg 12.88 r_dihedral_angle_3_deg 12.722 r_sphericity_free 6.08 r_dihedral_angle_1_deg 5.046 r_scangle_it 3.479 r_scbond_it 2.628 r_sphericity_bonded 2.407 r_mcangle_it 1.819 r_angle_refined_deg 1.601 r_angle_other_deg 1.555 r_mcbond_it 1.434 r_rigid_bond_restr 1.299 r_mcbond_other 0.483 r_symmetry_hbond_refined 0.294 r_nbd_refined 0.258 r_symmetry_vdw_other 0.217 r_chiral_restr 0.21 r_symmetry_vdw_refined 0.205 r_nbd_other 0.2 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.167 r_nbtor_other 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1792 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling REFMAC phasing