8IZG | pdb_00008izg

Crystal structure of intracellular B30.2 domain of BTN3A1 in complex with 5-HMBPP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5ZXK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP289Calcium acetate hydrate, PEG8000, Sodium citrate
Crystal Properties
Matthews coefficientSolvent content
2.550.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.6α = 90
b = 126.306β = 90
c = 39.405γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 9M2023-03-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE TPS 05A1.0NSRRCTPS 05A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.62599.40.04830.45.330828
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)
11.61.660.0109

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.622.1129248153199.010.129050.127460.130.161350.16RANDOM17.458
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]
0.040.12-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.362
r_dihedral_angle_2_deg7.37
r_dihedral_angle_1_deg6.834
r_rigid_bond_restr4.707
r_long_range_B_refined3.47
r_angle_other_deg3.098
r_long_range_B_other2.97
r_scangle_other1.983
r_angle_refined_deg1.664
r_scbond_it1.575
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.362
r_dihedral_angle_2_deg7.37
r_dihedral_angle_1_deg6.834
r_rigid_bond_restr4.707
r_long_range_B_refined3.47
r_angle_other_deg3.098
r_long_range_B_other2.97
r_scangle_other1.983
r_angle_refined_deg1.664
r_scbond_it1.575
r_scbond_other1.532
r_mcangle_it1.529
r_mcbond_it0.987
r_chiral_restr0.137
r_bond_other_d0.03
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_gen_planes_other0.003
r_dihedral_angle_4_deg
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_mcbond_other
r_mcangle_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1514
Nucleic Acid Atoms
Solvent Atoms204
Heterogen Atoms32

Software

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