7NZA

Structure of OBP1 from Varroa destructor, form P2<1>


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9.52932/3 of the initial crystallization conditions (CHES pH9.5, 0.1M, 30% PEG3000 w/v ) and 1/3 of ammonium sulfate screen (0.2 M sodium nitrate, 2.2M ammonium sulfate).
Crystal Properties
Matthews coefficientSolvent content
2.2344.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.604α = 90
b = 112.959β = 98.95
c = 41.817γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-08-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.9786SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.19940.197.20.0650.99813.15787891
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.191.2791.40.8850.7881.196.4

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 REPLACEMENTTHROUGHOUT7NYJ1.19938.8383470440297.230.180560.179470.20145RANDOM19.045
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]
0.010.01-0.090.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.984
r_dihedral_angle_4_deg18.367
r_dihedral_angle_3_deg11.984
r_dihedral_angle_1_deg5.433
r_long_range_B_refined4.713
r_long_range_B_other4.66
r_scangle_other3.448
r_scbond_it2.349
r_scbond_other2.348
r_angle_refined_deg2.197
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.984
r_dihedral_angle_4_deg18.367
r_dihedral_angle_3_deg11.984
r_dihedral_angle_1_deg5.433
r_long_range_B_refined4.713
r_long_range_B_other4.66
r_scangle_other3.448
r_scbond_it2.349
r_scbond_other2.348
r_angle_refined_deg2.197
r_angle_other_deg1.725
r_mcangle_other1.686
r_mcangle_it1.685
r_mcbond_it1.139
r_mcbond_other1.136
r_chiral_restr0.28
r_bond_refined_d0.018
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2213
Nucleic Acid Atoms
Solvent Atoms324
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing