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Crystal structure of a pheromone binding protein from Apis mellifera with a serendipitous ligand soaked at pH 4.0
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, SITTING DROP 4 293 1.7M ammonium sulfate, 0.1M sodium citrate, pH4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.06 59.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.374 α = 90 b = 84.671 β = 90 c = 46.263 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 4 tiroidal mirror 2007-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 1.9 46.27 100 0.101 0.101 16.1 8 13139 13139 21.49
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 1.9 2 100 0.464 0.464 4.1 8.1 1893
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 1.9 30 12133 12133 987 99.99 0.16574 0.16574 0.16283 0.1795 0.20243 0.213 RANDOM 12.51
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.867 r_dihedral_angle_1_deg 19.149 r_dihedral_angle_3_deg 14.58 r_dihedral_angle_4_deg 5.414 r_scangle_it 2.78 r_angle_other_deg 2.758 r_scbond_it 1.809 r_angle_refined_deg 1.497 r_mcangle_it 1.025 r_mcbond_it 0.537
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.867 r_dihedral_angle_1_deg 19.149 r_dihedral_angle_3_deg 14.58 r_dihedral_angle_4_deg 5.414 r_scangle_it 2.78 r_angle_other_deg 2.758 r_scbond_it 1.809 r_angle_refined_deg 1.497 r_mcangle_it 1.025 r_mcbond_it 0.537 r_mcbond_other 0.159 r_chiral_restr 0.119 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 919 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 50
Software Software Software Name Purpose ADSC data collection REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing