8BXV

Crystal structure of Odorant Binding Protein 5 from Anopheles gambiae (AgamOBP5) with Thymol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8BXU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.12M alcohols (0.02 M each of 1,6-Hexanediol, 1-Butanol, 1,2-Propanediol (racemic), 2-Propanol, 1,4- Butanediol and 1,3-Propanediol), 0.1 M MOPS/HEPES-Na pH 7.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD
Crystal Properties
Matthews coefficientSolvent content
2.448.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.241α = 90
b = 36.566β = 100.383
c = 54.962γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 9M2019-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91587DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.354.0694.30.99922.56.431153
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.3797.80.986.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.354.0631140158193.9480.1870.18510.220222.994
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]
-0.2210.2650.89-0.719
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.476
r_dihedral_angle_4_deg16.419
r_dihedral_angle_3_deg14.105
r_dihedral_angle_1_deg6.396
r_lrange_it6.097
r_lrange_other6.006
r_scangle_it4.349
r_scangle_other4.347
r_scbond_it2.996
r_scbond_other2.994
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.476
r_dihedral_angle_4_deg16.419
r_dihedral_angle_3_deg14.105
r_dihedral_angle_1_deg6.396
r_lrange_it6.097
r_lrange_other6.006
r_scangle_it4.349
r_scangle_other4.347
r_scbond_it2.996
r_scbond_other2.994
r_mcangle_it2.601
r_mcangle_other2.6
r_angle_refined_deg1.958
r_mcbond_other1.807
r_mcbond_it1.803
r_angle_other_deg1.541
r_nbd_refined0.295
r_nbd_other0.2
r_symmetry_nbd_other0.188
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.155
r_symmetry_xyhbond_nbd_refined0.121
r_metal_ion_refined0.12
r_symmetry_nbd_refined0.108
r_chiral_restr0.092
r_symmetry_nbtor_other0.089
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms973
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing