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Structure of Pyruvate dehydrogenase phosphatase regulatory subunit epitope presented by H2-Dd
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8D5F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298.15 0.2M Potassium thiocyanate and 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.8 56.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.415 α = 90 b = 104.564 β = 90 c = 169.993 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 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 1.801 50 99 0.177 0.185 0.052 0.998 13.2 13.2 81134
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 1.89 1.93 82.6 0.261 11.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.801 49.819 69254 3480 73.729 0.21 0.2081 0.2488 0.23 30.284
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] -0.64 0.722 -0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.76 r_dihedral_angle_3_deg 16.878 r_dihedral_angle_2_deg 15.746 r_lrange_it 7.833 r_dihedral_angle_1_deg 7.362 r_scangle_it 6.154 r_scbond_it 4.175 r_mcangle_it 3.453 r_mcbond_it 2.444 r_angle_refined_deg 2.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.76 r_dihedral_angle_3_deg 16.878 r_dihedral_angle_2_deg 15.746 r_lrange_it 7.833 r_dihedral_angle_1_deg 7.362 r_scangle_it 6.154 r_scbond_it 4.175 r_mcangle_it 3.453 r_mcbond_it 2.444 r_angle_refined_deg 2.237 r_nbtor_refined 0.303 r_xyhbond_nbd_refined 0.232 r_nbd_refined 0.214 r_symmetry_nbd_refined 0.176 r_ncsr_local_group_1 0.14 r_metal_ion_refined 0.138 r_chiral_restr 0.133 r_ncsr_local_group_2 0.131 r_symmetry_xyhbond_nbd_refined 0.125 r_gen_planes_refined 0.015 r_bond_refined_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6141 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction BUCCANEER model building PHASER phasing