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Crystal structure of intracellular B30.2 domain of BTN3A3 mutant in complex with HMBPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N7U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 Isopropanol ,Imidazole, PEG 8000
Crystal Properties Matthews coefficient Solvent content 1.76 30.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.797 α = 73.23 b = 41.392 β = 89.87 c = 62.49 γ = 68.95
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-300 2017-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1 NSRRC BL15A1
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 2 25 84.2 0.08 16.06 3 20422
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 0.946
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4N7U 2 25 19413 997 81.68 0.1942 0.19091 0.1982 0.25662 0.2587 RANDOM 25.298
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] -0.31 0.67 -0.14 -0.36 1.33 1.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.172 r_dihedral_angle_4_deg 19.529 r_dihedral_angle_3_deg 15.886 r_dihedral_angle_1_deg 8.21 r_long_range_B_refined 5.445 r_long_range_B_other 5.444 r_scangle_other 4.497 r_mcangle_it 3.273 r_mcangle_other 3.272 r_scbond_it 3.227
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.172 r_dihedral_angle_4_deg 19.529 r_dihedral_angle_3_deg 15.886 r_dihedral_angle_1_deg 8.21 r_long_range_B_refined 5.445 r_long_range_B_other 5.444 r_scangle_other 4.497 r_mcangle_it 3.273 r_mcangle_other 3.272 r_scbond_it 3.227 r_scbond_other 3.226 r_mcbond_it 2.602 r_mcbond_other 2.602 r_angle_refined_deg 1.174 r_angle_other_deg 0.635 r_chiral_restr 0.076 r_gen_planes_refined 0.013 r_bond_refined_d 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 Atoms Number Protein Atoms 3102 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing