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Crystal structure of intracellular B30.2 domain of BTN3A1 in complex with 5-HMBPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZXK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 Calcium acetate hydrate, PEG8000, Sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.5 50.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.6 α = 90 b = 126.306 β = 90 c = 39.405 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 X 9M 2023-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1.0 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.6 25 99.4 0.048 30.4 5.3 30828
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.66 0.0109
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.6 22.11 29248 1531 99.01 0.12905 0.12746 0.1277 0.16135 0.1615 RANDOM 17.458
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] 0.04 0.12 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.362 r_dihedral_angle_2_deg 7.37 r_dihedral_angle_1_deg 6.834 r_rigid_bond_restr 4.707 r_long_range_B_refined 3.47 r_angle_other_deg 3.098 r_long_range_B_other 2.97 r_scangle_other 1.983 r_angle_refined_deg 1.664 r_scbond_it 1.575
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.362 r_dihedral_angle_2_deg 7.37 r_dihedral_angle_1_deg 6.834 r_rigid_bond_restr 4.707 r_long_range_B_refined 3.47 r_angle_other_deg 3.098 r_long_range_B_other 2.97 r_scangle_other 1.983 r_angle_refined_deg 1.664 r_scbond_it 1.575 r_scbond_other 1.532 r_mcangle_it 1.529 r_mcbond_it 0.987 r_chiral_restr 0.137 r_bond_other_d 0.03 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 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 Atoms Number Protein Atoms 1514 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing