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The complex of Pre-mRNA-Processing Factor 19 (Prpf19) neoantigen KYLQVASHV Presented by H2-Kd
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VGK PDB entry 1VGK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277.15 20% w/v PEG3000, 100 mM HEPES, 200 mM sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.4336634 49.490311
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.44 α = 90 b = 66.57 β = 92.01 c = 56.96 γ = 90
Symmetry Space Group C 1 2 1
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 2020-11-23 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 1.95 40.902 97.1 0.138 0.173 0.103 0.991 15.9 4.7 30593
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 1.95 2 0.74 0.954 0.594 0.682 4
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1VGK 1.95 40.902 30593 1561 96.868 0.188 0.186 0.1956 0.2297 0.2437 39.061
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] -0.596 0.062 0.595 -0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.761 r_dihedral_angle_3_deg 15.184 r_dihedral_angle_2_deg 12.567 r_lrange_it 8.419 r_dihedral_angle_1_deg 6.622 r_scangle_it 6.137 r_scbond_it 4.027 r_mcangle_it 3.907 r_mcbond_it 2.666 r_angle_refined_deg 1.701
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.761 r_dihedral_angle_3_deg 15.184 r_dihedral_angle_2_deg 12.567 r_lrange_it 8.419 r_dihedral_angle_1_deg 6.622 r_scangle_it 6.137 r_scbond_it 4.027 r_mcangle_it 3.907 r_mcbond_it 2.666 r_angle_refined_deg 1.701 r_nbtor_refined 0.312 r_symmetry_xyhbond_nbd_refined 0.253 r_symmetry_nbd_refined 0.227 r_nbd_refined 0.225 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.111 r_gen_planes_refined 0.009 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3151 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement REFMAC refinement SCALEPACK data scaling PHASER phasing BUCCANEER model building