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Dimeric crystal structure of a pheromone binding protein from Apis mellifera at pH 7.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CZY PDB ENTRY 3CZY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.2M Magnesium chloride, 0.1M Tris, 17% PEG8000, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.16 43.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.862 α = 90 b = 75.513 β = 90 c = 84.307 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 2006-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.886 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 2.5 35 99.9 0.115 0.115 14.6 6.2 8426 8426 30.15
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) 2.5 2.64 100 0.313 0.313 5.1 6.5 1214
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 3CZY 2.5 35 7568 7568 826 100 0.22578 0.22578 0.22017 0.2269 0.27838 0.2931 RANDOM 12.893
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] 1.85 -1.54 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.272 r_dihedral_angle_3_deg 12.831 r_dihedral_angle_4_deg 6.888 r_dihedral_angle_1_deg 6.083 r_scangle_it 1.802 r_scbond_it 1.275 r_angle_refined_deg 1.213 r_angle_other_deg 0.866 r_mcangle_it 0.659 r_mcbond_it 0.624
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.272 r_dihedral_angle_3_deg 12.831 r_dihedral_angle_4_deg 6.888 r_dihedral_angle_1_deg 6.083 r_scangle_it 1.802 r_scbond_it 1.275 r_angle_refined_deg 1.213 r_angle_other_deg 0.866 r_mcangle_it 0.659 r_mcbond_it 0.624 r_symmetry_vdw_other 0.35 r_symmetry_vdw_refined 0.279 r_nbd_refined 0.212 r_nbd_other 0.184 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.169 r_mcbond_other 0.101 r_nbtor_other 0.087 r_chiral_restr 0.065 r_symmetry_hbond_refined 0.038 r_bond_refined_d 0.012 r_bond_other_d 0.006 r_gen_planes_refined 0.004 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1813 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling REFMAC phasing