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Crystal structure of a pheromone binding protein mutant D35N, from Apis mellifera, soaked at pH 4.0
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 4 293 1.3M ammonium sulfate, 67mM sodium citrate, 33mM SPG buffer, 8.3% PEG1500, pH5.5, crystal was soaked in the same condition at pH4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3 58.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.215 α = 90 b = 83.999 β = 90 c = 47.54 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 315 Tiroidal mirror 2008-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.979 ESRF ID29
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 1.7 57.64 99.1 0.047 0.047 26.4 6.8 17650 17650 24.53
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) 1.7 1.79 99.6 0.349 0.349 4.5 7 2545
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 1.7 30 16595 16595 1044 98.96 0.16309 0.16309 0.16133 0.1745 0.19131 0.2028 RANDOM 24.694
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] -0.63 0.44 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.677 r_dihedral_angle_3_deg 14.449 r_dihedral_angle_1_deg 13.982 r_sphericity_free 7.75 r_dihedral_angle_4_deg 7.465 r_rigid_bond_restr 3.941 r_scangle_it 3.928 r_sphericity_bonded 3.807 r_scbond_it 3.086 r_angle_refined_deg 2.211
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.677 r_dihedral_angle_3_deg 14.449 r_dihedral_angle_1_deg 13.982 r_sphericity_free 7.75 r_dihedral_angle_4_deg 7.465 r_rigid_bond_restr 3.941 r_scangle_it 3.928 r_sphericity_bonded 3.807 r_scbond_it 3.086 r_angle_refined_deg 2.211 r_mcangle_it 2.086 r_angle_other_deg 1.918 r_mcbond_it 1.346 r_mcbond_other 0.635 r_symmetry_vdw_refined 0.394 r_symmetry_hbond_refined 0.284 r_nbd_refined 0.269 r_symmetry_vdw_other 0.258 r_xyhbond_nbd_refined 0.232 r_nbd_other 0.207 r_nbtor_refined 0.192 r_chiral_restr 0.104 r_nbtor_other 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 947 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling REFMAC phasing