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Crystal structure of a pheromone binding protein from Apis mellifera soaked at pH 4.0
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 4 293 1.9M ammonium sulfate, 0.1M sodium citrate, pH5.5, crystal was soaked in the same condition at pH4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.97 58.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.146 α = 90 b = 83.53 β = 90 c = 47.361 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 4r Tiroidal mirror 2007-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3
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 57.45 99.8 0.069 0.069 15.3 5 10923 10923 31.18
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 2 2.11 100 0.46 0.46 3.4 5 7880
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 2 40 9844 9844 1075 99.64 0.17382 0.17382 0.17068 0.1833 0.20315 0.2204 RANDOM 65.231
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] 0.57 -0.36 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.899 r_dihedral_angle_3_deg 14.544 r_dihedral_angle_4_deg 10.633 r_dihedral_angle_1_deg 5.891 r_scangle_it 2.372 r_scbond_it 1.669 r_angle_refined_deg 1.3 r_mcangle_it 1.063 r_angle_other_deg 0.937 r_mcbond_it 0.888
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.899 r_dihedral_angle_3_deg 14.544 r_dihedral_angle_4_deg 10.633 r_dihedral_angle_1_deg 5.891 r_scangle_it 2.372 r_scbond_it 1.669 r_angle_refined_deg 1.3 r_mcangle_it 1.063 r_angle_other_deg 0.937 r_mcbond_it 0.888 r_symmetry_hbond_refined 0.342 r_symmetry_vdw_refined 0.245 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.209 r_mcbond_other 0.204 r_nbd_other 0.192 r_nbtor_refined 0.182 r_symmetry_vdw_other 0.176 r_nbtor_other 0.09 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 899 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling REFMAC phasing