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Dimeric crystal structure of a pheromone binding protein mutant D35N, from apis mellifera, at pH 7.0
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 7 293 2.1M ammonium sulfate, 0.2M di ammonium phosphate, 20mM di sodium phosphate, pH7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.05 40.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.054 α = 90 b = 60.948 β = 90 c = 57.334 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 CCD ADSC QUANTUM 315 Tiroidal mirror 2008-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.984 ESRF ID23-2
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 1.55 50 99.6 0.048 0.048 20.3 4.4 32103 32103 18.48
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) 1.55 1.63 99.6 0.321 0.321 3.8 4.2 4588
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 1.6 15 28039 28039 1200 99.54 0.16088 0.16088 0.15897 0.2132 0.20597 0.257 RANDOM 21.421
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] 1.17 -2.08 0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.605 r_dihedral_angle_4_deg 14.447 r_dihedral_angle_3_deg 11.01 r_dihedral_angle_1_deg 10.304 r_sphericity_free 6.128 r_scangle_it 3.187 r_scbond_it 2.546 r_sphericity_bonded 2.272 r_mcangle_it 1.562 r_angle_refined_deg 1.498
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.605 r_dihedral_angle_4_deg 14.447 r_dihedral_angle_3_deg 11.01 r_dihedral_angle_1_deg 10.304 r_sphericity_free 6.128 r_scangle_it 3.187 r_scbond_it 2.546 r_sphericity_bonded 2.272 r_mcangle_it 1.562 r_angle_refined_deg 1.498 r_rigid_bond_restr 1.298 r_mcbond_it 1.261 r_angle_other_deg 0.985 r_mcbond_other 0.434 r_xyhbond_nbd_refined 0.271 r_symmetry_hbond_refined 0.244 r_nbd_refined 0.239 r_symmetry_vdw_other 0.236 r_symmetry_vdw_refined 0.209 r_nbd_other 0.204 r_nbtor_refined 0.183 r_nbtor_other 0.086 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1905 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling REFMAC phasing