6ITA | pdb_00006ita

Crystal structure of intracellular B30.2 domain of BTN3A1 mutant


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291Sodium Fluoride, Polyethylene Glycol 3350
Crystal Properties
Matthews coefficientSolvent content
1.9537.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.961α = 90
b = 46.961β = 90
c = 158.996γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002018-11-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A11NSRRCBL15A1

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
11.245.0498.620.03957.278.952887
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)
11.21.240.4520.964

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4N7U1.245.0452887274398.620.204250.202780.210.231860.24RANDOM18.21
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]
-0.67-0.671.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.699
r_dihedral_angle_4_deg22.781
r_dihedral_angle_3_deg14.316
r_dihedral_angle_1_deg8.368
r_long_range_B_refined6.2
r_long_range_B_other5.987
r_scangle_other4.289
r_scbond_it2.961
r_scbond_other2.946
r_mcangle_other2.589
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.699
r_dihedral_angle_4_deg22.781
r_dihedral_angle_3_deg14.316
r_dihedral_angle_1_deg8.368
r_long_range_B_refined6.2
r_long_range_B_other5.987
r_scangle_other4.289
r_scbond_it2.961
r_scbond_other2.946
r_mcangle_other2.589
r_mcangle_it2.584
r_mcbond_it1.973
r_mcbond_other1.958
r_angle_refined_deg1.721
r_angle_other_deg0.825
r_chiral_restr0.124
r_bond_refined_d0.016
r_gen_planes_refined0.015
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms1513
Nucleic Acid Atoms
Solvent Atoms308
Heterogen Atoms

Software

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