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Bombyx mori pheromone binding protein bound to iodohexadecane
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DQE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 PEG 4000, Tris, MgSO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.05 40.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.79 α = 90 b = 83.79 β = 90 c = 34.88 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.95 CHESS F1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.006 59.76 92 13400 11314 2 26
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1DQE 2.006 59.76 8056 392 97.21 0.223 0.223 0.22 0.2281 0.265 0.2609 RANDOM 29.882
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] -0.68 -0.68 1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.943 r_scangle_it 6.228 r_scbond_it 4.331 r_mcangle_it 3.109 r_angle_refined_deg 2.815 r_mcbond_it 1.863 r_angle_other_deg 1.334 r_symmetry_vdw_other 0.32 r_nbd_refined 0.293 r_nbd_other 0.256
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.943 r_scangle_it 6.228 r_scbond_it 4.331 r_mcangle_it 3.109 r_angle_refined_deg 2.815 r_mcbond_it 1.863 r_angle_other_deg 1.334 r_symmetry_vdw_other 0.32 r_nbd_refined 0.293 r_nbd_other 0.256 r_xyhbond_nbd_refined 0.208 r_symmetry_vdw_refined 0.187 r_chiral_restr 0.181 r_symmetry_hbond_refined 0.129 r_nbtor_other 0.105 r_bond_refined_d 0.038 r_gen_planes_other 0.032 r_gen_planes_refined 0.021 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1038 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 17
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection