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Crystal structure of intracellular B30.2 domain of BTN3A3
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 291 SODIUM CITRATE, IMIDAZOLE PH 8.0, 1
-PROPANOL., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K
Crystal Properties Matthews coefficient Solvent content 2.54 51.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.308 α = 90 b = 50.308 β = 90 c = 261.093 γ = 90
Symmetry Space Group P 43 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 PSI PILATUS 6M 2017-01-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9793 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 3 50 100 0.994 46.625 23.6 7487
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 3 3.05 100 0.654
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 3 50 7044 374 100 0.199 0.195 0.2036 0.275 0.2715 RANDOM 98.74
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] 6.54 6.54 -13.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.674 r_dihedral_angle_4_deg 21.485 r_dihedral_angle_3_deg 19.224 r_long_range_B_refined 14.46 r_long_range_B_other 14.456 r_mcangle_it 11.634 r_mcangle_other 11.63 r_scangle_other 11.603 r_mcbond_it 8.397 r_mcbond_other 8.388
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.674 r_dihedral_angle_4_deg 21.485 r_dihedral_angle_3_deg 19.224 r_long_range_B_refined 14.46 r_long_range_B_other 14.456 r_mcangle_it 11.634 r_mcangle_other 11.63 r_scangle_other 11.603 r_mcbond_it 8.397 r_mcbond_other 8.388 r_dihedral_angle_1_deg 8.198 r_scbond_it 8.114 r_scbond_other 8.11 r_angle_refined_deg 1.909 r_angle_other_deg 1.043 r_chiral_restr 0.096 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 1552 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing REFMAC refinement