6ISM | pdb_00006ism

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 DROP291Magnesium chloride hexahydrate, HEPES pH 7.5, Polyethylene glycol monomethyl ether 550
Crystal Properties
Matthews coefficientSolvent content
1.7931.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.029α = 90
b = 54.305β = 90
c = 63.027γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002018-10-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE TPS 05A1NSRRCTPS 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
11.2541.1497.990.0553.6910.742394
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)
11.251.290.2880.914

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 REPLACEMENTTHROUGHOUT4N7U1.2541.1442394215597.990.175130.17360.180.205210.21RANDOM17.721
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]
0.02-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.935
r_dihedral_angle_4_deg17.155
r_dihedral_angle_3_deg13.689
r_dihedral_angle_1_deg7.934
r_long_range_B_refined6.512
r_long_range_B_other6.416
r_scangle_other4.854
r_scbond_it3.403
r_scbond_other3.401
r_mcangle_other2.898
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.935
r_dihedral_angle_4_deg17.155
r_dihedral_angle_3_deg13.689
r_dihedral_angle_1_deg7.934
r_long_range_B_refined6.512
r_long_range_B_other6.416
r_scangle_other4.854
r_scbond_it3.403
r_scbond_other3.401
r_mcangle_other2.898
r_mcangle_it2.897
r_mcbond_it1.989
r_mcbond_other1.981
r_angle_refined_deg1.717
r_angle_other_deg0.79
r_chiral_restr0.122
r_bond_refined_d0.017
r_gen_planes_refined0.016
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 Atoms1497
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms

Software

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