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Crystal structure of a pheromone binding protein mutant D35N, from Apis mellifera, soaked at pH 7.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D75 PDB ENTRY 3D75
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 1.3M ammonium sulfate, 67mM sodium citrate, 33mM SPG buffer, 8.3% PEG1500, pH5.5, crystal was soaked in the same condition at pH7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3 58.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.991 α = 90 b = 84.196 β = 90 c = 47.558 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 IMAGE PLATE MAR scanner 345 mm plate polar mirror 2008-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.542
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 25.13 99.8 0.056 0.056 24.8 6.1 12833 12833 22.88
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) 1.9 2 100 0.322 0.322 6.5 6 1837
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 3D75 1.9 15 11728 11728 947 98.85 0.19423 0.19423 0.19044 0.2341 0.24146 0.2758 RANDOM 26.522
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] -0.55 -0.56 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.675 r_dihedral_angle_3_deg 14.019 r_dihedral_angle_4_deg 12.491 r_dihedral_angle_1_deg 6.516 r_scangle_it 2.572 r_angle_refined_deg 1.848 r_scbond_it 1.638 r_angle_other_deg 1.276 r_mcangle_it 1.05 r_mcbond_it 0.626
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.675 r_dihedral_angle_3_deg 14.019 r_dihedral_angle_4_deg 12.491 r_dihedral_angle_1_deg 6.516 r_scangle_it 2.572 r_angle_refined_deg 1.848 r_scbond_it 1.638 r_angle_other_deg 1.276 r_mcangle_it 1.05 r_mcbond_it 0.626 r_chiral_restr 0.29 r_symmetry_hbond_refined 0.264 r_symmetry_vdw_refined 0.263 r_xyhbond_nbd_refined 0.237 r_nbd_refined 0.231 r_nbd_other 0.209 r_nbtor_refined 0.185 r_symmetry_vdw_other 0.181 r_mcbond_other 0.162 r_nbtor_other 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 910 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection MOSFLM data reduction SCALA data scaling REFMAC phasing