6J06 | pdb_00006j06

Crystal structure of intracellular B30.2 domain of BTN3A1 in complex with HMBPP-08


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP298Lithium Sulfate monohydrate, tri-Sodium Citrate dihydrate, Ammonium Sulfate
Crystal Properties
Matthews coefficientSolvent content
4.9475.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.929α = 90
b = 211.588β = 90
c = 56.269γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002018-01-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A11.0NSRRCBL15A1

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
12.652399.80.06436.186.540042
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.652.740.923

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 REPLACEMENTTHROUGHOUT4N7U2.652338016196799.520.174290.171730.180.223460.23RANDOM57.223
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]
4.51-0.47-4.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.577
r_dihedral_angle_3_deg19.839
r_dihedral_angle_4_deg16.539
r_long_range_B_other13.222
r_long_range_B_refined13.209
r_scangle_other12.026
r_scbond_it9.5
r_scbond_other9.45
r_dihedral_angle_1_deg9.192
r_mcangle_it8.718
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.577
r_dihedral_angle_3_deg19.839
r_dihedral_angle_4_deg16.539
r_long_range_B_other13.222
r_long_range_B_refined13.209
r_scangle_other12.026
r_scbond_it9.5
r_scbond_other9.45
r_dihedral_angle_1_deg9.192
r_mcangle_it8.718
r_mcangle_other8.718
r_mcbond_it6.952
r_mcbond_other6.94
r_angle_refined_deg1.425
r_angle_other_deg0.682
r_chiral_restr0.087
r_gen_planes_refined0.016
r_bond_refined_d0.011
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 Atoms4542
Nucleic Acid Atoms
Solvent Atoms201
Heterogen Atoms145

Software

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