5ZZ3

Crystal structure of intracellular B30.2 domain of BTN3A3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4N7U 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291SODIUM CITRATE, IMIDAZOLE PH 8.0, 1 -PROPANOL., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K
Crystal Properties
Matthews coefficientSolvent content
2.5451.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.308α = 90
b = 50.308β = 90
c = 261.093γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2017-01-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.9793SSRFBL19U1

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
13501000.99446.62523.67487
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.051000.654

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 REPLACEMENTTHROUGHOUT4N7U35070443741000.1990.1950.275RANDOM98.74
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]
6.546.54-13.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.674
r_dihedral_angle_4_deg21.485
r_dihedral_angle_3_deg19.224
r_long_range_B_refined14.46
r_long_range_B_other14.456
r_mcangle_it11.634
r_mcangle_other11.63
r_scangle_other11.603
r_mcbond_it8.397
r_mcbond_other8.388
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.674
r_dihedral_angle_4_deg21.485
r_dihedral_angle_3_deg19.224
r_long_range_B_refined14.46
r_long_range_B_other14.456
r_mcangle_it11.634
r_mcangle_other11.63
r_scangle_other11.603
r_mcbond_it8.397
r_mcbond_other8.388
r_dihedral_angle_1_deg8.198
r_scbond_it8.114
r_scbond_other8.11
r_angle_refined_deg1.909
r_angle_other_deg1.043
r_chiral_restr0.096
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms1552
Nucleic Acid Atoms
Solvent Atoms8
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMACrefinement