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Crystal structure of a pheromone binding protein mutant D35A, from Apis mellifera, soaked at pH 5.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D73 PDB ENTRY 3D73
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 2.1M ammonium sulfate, 0.2M di-ammonium phosphate, 20mM di-sodium phosphate, pH7.0, crystal was soaked in the same condition at pH5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.99 38.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.133 α = 90 b = 60.769 β = 90 c = 56.27 γ = 90
Symmetry Space Group P 21 21 2
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 2008-01-21 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 2.1 30.39 99.8 0.066 0.066 14.5 3.9 12708 12708 24.26
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) 2.1 2.21 100 0.29 0.29 4.3 3.8 1804
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 3D73 2.1 15 11717 11717 949 99.63 0.17886 0.17886 0.17472 0.2206 0.22921 0.2557 RANDOM 28.728
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] 2.61 -2.3 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.55 r_dihedral_angle_4_deg 19.016 r_dihedral_angle_3_deg 12.851 r_dihedral_angle_1_deg 9.154 r_scangle_it 2.509 r_scbond_it 2.048 r_angle_refined_deg 1.469 r_angle_other_deg 1.004 r_mcbond_it 0.881 r_mcangle_it 0.867
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.55 r_dihedral_angle_4_deg 19.016 r_dihedral_angle_3_deg 12.851 r_dihedral_angle_1_deg 9.154 r_scangle_it 2.509 r_scbond_it 2.048 r_angle_refined_deg 1.469 r_angle_other_deg 1.004 r_mcbond_it 0.881 r_mcangle_it 0.867 r_nbd_refined 0.233 r_nbd_other 0.2 r_symmetry_vdw_other 0.192 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.179 r_symmetry_hbond_refined 0.178 r_mcbond_other 0.158 r_chiral_restr 0.1 r_symmetry_vdw_refined 0.093 r_nbtor_other 0.089 r_bond_refined_d 0.012 r_bond_other_d 0.008 r_gen_planes_refined 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1845 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection MOSFLM data reduction SCALA data scaling REFMAC phasing