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Crystal structure of intracellular B30.2 domain of BTN3A1 in complex with HMBPP-08
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 Lithium Sulfate monohydrate, tri-Sodium Citrate dihydrate, Ammonium Sulfate
Crystal Properties Matthews coefficient Solvent content 4.94 75.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.929 α = 90 b = 211.588 β = 90 c = 56.269 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 CCD RAYONIX MX-300 2018-01-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.0 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 2.65 23 99.8 0.064 36.18 6.5 40042
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 2.65 2.74 0.923
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 2.65 23 38016 1967 99.52 0.17429 0.17173 0.1791 0.22346 0.2276 RANDOM 57.223
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.577 r_dihedral_angle_3_deg 19.839 r_dihedral_angle_4_deg 16.539 r_long_range_B_other 13.222 r_long_range_B_refined 13.209 r_scangle_other 12.026 r_scbond_it 9.5 r_scbond_other 9.45 r_dihedral_angle_1_deg 9.192 r_mcangle_it 8.718
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.577 r_dihedral_angle_3_deg 19.839 r_dihedral_angle_4_deg 16.539 r_long_range_B_other 13.222 r_long_range_B_refined 13.209 r_scangle_other 12.026 r_scbond_it 9.5 r_scbond_other 9.45 r_dihedral_angle_1_deg 9.192 r_mcangle_it 8.718 r_mcangle_other 8.718 r_mcbond_it 6.952 r_mcbond_other 6.94 r_angle_refined_deg 1.425 r_angle_other_deg 0.682 r_chiral_restr 0.087 r_gen_planes_refined 0.016 r_bond_refined_d 0.011 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 4542 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 145
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing