2P70

Bombyx mori pheromone binding protein bound to bell pepper odorant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DQE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8295PEG 4000, Tris, MgSO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.0540.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.85α = 90
b = 83.85β = 90
c = 34.82γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F10.95CHESSF1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.159.76940.1150.1153.77724565552.730.99

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1DQE2.159.76686631194.740.2050.2030.247RANDOM32.677
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]
-1.23-1.232.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.253
r_scangle_it6.505
r_scbond_it4.474
r_mcangle_it3.152
r_angle_refined_deg2.918
r_mcbond_it1.87
r_angle_other_deg1.556
r_symmetry_vdw_refined0.316
r_nbd_other0.271
r_nbd_refined0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.253
r_scangle_it6.505
r_scbond_it4.474
r_mcangle_it3.152
r_angle_refined_deg2.918
r_mcbond_it1.87
r_angle_other_deg1.556
r_symmetry_vdw_refined0.316
r_nbd_other0.271
r_nbd_refined0.27
r_symmetry_vdw_other0.267
r_chiral_restr0.195
r_xyhbond_nbd_refined0.164
r_nbtor_other0.118
r_symmetry_hbond_refined0.064
r_bond_refined_d0.046
r_gen_planes_other0.024
r_gen_planes_refined0.019
r_bond_other_d0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1038
Nucleic Acid Atoms
Solvent Atoms28
Heterogen Atoms24

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection