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Structure of pyruvate dehydrogenase phosphatase regulatory subunit neoepitope presented by H2-Dd
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8D5F PDB entry 8D5F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 0.2 M sodium isothiocyanate, 20% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.4 48.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.091 α = 90 b = 86.359 β = 90 c = 211.581 γ = 90
Symmetry Space Group C 2 2 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 EIGER2 X 16M 2022-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979180 APS 24-ID-C
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 41.343 99.8 0.187 0.195 0.055 0.997 10.3 13.1 29908
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 2.05 0.367
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 FREE R-VALUE PDB entry 8D5F 2.194 41.343 22463 1110 99.113 0.212 0.2096 0.2139 0.2479 0.25 50.643
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] -2.124 5.423 -3.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.435 r_dihedral_angle_3_deg 14.886 r_dihedral_angle_2_deg 13.319 r_lrange_it 10.451 r_scangle_it 7.408 r_dihedral_angle_1_deg 6.992 r_scbond_it 5.18 r_mcangle_it 5.008 r_mcbond_it 3.582 r_angle_refined_deg 1.392
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.435 r_dihedral_angle_3_deg 14.886 r_dihedral_angle_2_deg 13.319 r_lrange_it 10.451 r_scangle_it 7.408 r_dihedral_angle_1_deg 6.992 r_scbond_it 5.18 r_mcangle_it 5.008 r_mcbond_it 3.582 r_angle_refined_deg 1.392 r_nbtor_refined 0.306 r_xyhbond_nbd_refined 0.291 r_nbd_refined 0.22 r_symmetry_xyhbond_nbd_refined 0.175 r_symmetry_nbd_refined 0.133 r_chiral_restr 0.086 r_metal_ion_refined 0.061 r_gen_planes_refined 0.009 r_bond_refined_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2822 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing