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Crystal Structure of GTP-bound Irgb6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TQD 1TQD, 1TPZ, 1TQ2 experimental model PDB 1TPZ 1TQD, 1TPZ, 1TQ2 experimental model PDB 1TQ2 1TQD, 1TPZ, 1TQ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Sodium Citrate, Polyethylene Glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.25 45.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.618 α = 90 b = 75.743 β = 90 c = 80.62 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 9M 2020-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.000 SPring-8 BL32XU
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 1.51 43.29 99.9 0.999 15.07 6.99 129901
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 1.51 1.6 0.524
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 1TQD, 1TPZ, 1TQ2 1.51 43.29 65855 1997 99.94 0.14831 0.14686 0.1459 0.19687 0.1955 RANDOM 33.227
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] 0.74 -0.8 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.143 r_dihedral_angle_4_deg 23.322 r_dihedral_angle_3_deg 14.01 r_long_range_B_refined 8.115 r_scangle_other 8.05 r_long_range_B_other 8.033 r_mcangle_it 6.99 r_mcangle_other 6.989 r_scbond_it 6.727 r_scbond_other 6.727
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.143 r_dihedral_angle_4_deg 23.322 r_dihedral_angle_3_deg 14.01 r_long_range_B_refined 8.115 r_scangle_other 8.05 r_long_range_B_other 8.033 r_mcangle_it 6.99 r_mcangle_other 6.989 r_scbond_it 6.727 r_scbond_other 6.727 r_mcbond_it 5.683 r_dihedral_angle_1_deg 5.673 r_mcbond_other 5.656 r_rigid_bond_restr 4.468 r_angle_refined_deg 1.768 r_angle_other_deg 1.468 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3304 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHENIX phasing