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The complex of Gtf2b neoantigen TGAARFDEF Presented by H2-Dd
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KD7 {DB entry 5KD7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 309.15 20% PEG3350, 200 nM sodium tartrate dibasic dihydrate
Crystal Properties Matthews coefficient Solvent content 2.21 44.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.3 α = 90 b = 68.86 β = 90 c = 109.44 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 16M 2019-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-E 0.98 APS 21-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.31 47.233 99.2 0.12 0.143 0.077 0.993 10.7 6 17756 29.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.31 2.39 0.046 0.054 0.027 0.996 6
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 (All) 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 {DB entry 5KD7 2.31 47.233 17755 891 98.875 0.193 0.193 0.1916 0.1991 0.1943 RANDOM 35.928
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] -0.492 0.358 0.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.552 r_dihedral_angle_3_deg 18.254 r_dihedral_angle_1_deg 7.3 r_lrange_it 7.202 r_scangle_it 4.14 r_mcangle_it 2.937 r_scbond_it 2.508 r_dihedral_angle_2_deg 2.091 r_angle_refined_deg 1.979 r_mcbond_it 1.718
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.552 r_dihedral_angle_3_deg 18.254 r_dihedral_angle_1_deg 7.3 r_lrange_it 7.202 r_scangle_it 4.14 r_mcangle_it 2.937 r_scbond_it 2.508 r_dihedral_angle_2_deg 2.091 r_angle_refined_deg 1.979 r_mcbond_it 1.718 r_nbtor_refined 0.309 r_nbd_refined 0.22 r_symmetry_nbd_refined 0.182 r_xyhbond_nbd_refined 0.141 r_symmetry_xyhbond_nbd_refined 0.129 r_chiral_restr 0.126 r_bond_refined_d 0.011 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3134 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PHASER phasing