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Crystal structure of a pheromone binding protein from Apis mellifera soaked at pH 7.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BJH PDB ENTRY 3BJH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 1.7M ammonium sulfate, 0.1M sodium citrate, pH5.5, crystal was soaked in same conditions at pH7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.05 59.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.478 α = 90 b = 86.185 β = 90 c = 49.557 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 cylindrical gazing incidence mirror 2007-09-07 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 1.95 56.8 99.9 0.06 0.06 21.8 5.9 12126 12126 29.57
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 1.95 2.06 99.9 0.413 0.413 4.1 5.9 1733
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 3BJH 1.95 20 11121 11121 976 99.88 0.17848 0.17848 0.17511 0.1872 0.21714 0.2232 RANDOM 37.149
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] 0.18 -1.77 1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.114 r_dihedral_angle_3_deg 13.151 r_dihedral_angle_4_deg 7.026 r_dihedral_angle_1_deg 5.165 r_scangle_it 2.164 r_scbond_it 1.559 r_angle_refined_deg 1.362 r_mcangle_it 1.011 r_angle_other_deg 0.948 r_mcbond_it 0.812
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.114 r_dihedral_angle_3_deg 13.151 r_dihedral_angle_4_deg 7.026 r_dihedral_angle_1_deg 5.165 r_scangle_it 2.164 r_scbond_it 1.559 r_angle_refined_deg 1.362 r_mcangle_it 1.011 r_angle_other_deg 0.948 r_mcbond_it 0.812 r_symmetry_vdw_refined 0.239 r_symmetry_vdw_other 0.225 r_nbd_refined 0.213 r_symmetry_hbond_refined 0.208 r_xyhbond_nbd_refined 0.197 r_mcbond_other 0.193 r_nbd_other 0.19 r_nbtor_refined 0.177 r_nbtor_other 0.091 r_chiral_restr 0.086 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 907 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling REFMAC phasing