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Human octameric PAICS in complex with SAICAR, AMP-PNP, and magnesium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H31
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 6 mg/ml PAICS with 5 mM SAICAR, 5 mM AMP-PNP, and 10 mM MgCl2; 0.1 M MES/imidazole pH 6.5, 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, and 0.02 M sodium oxamate
Crystal Properties Matthews coefficient Solvent content 2.8 56.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.263 α = 90 b = 154.019 β = 90 c = 223.624 γ = 90
Symmetry Space Group I 2 2 2
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 PILATUS3 6M 2018-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.406 47.33 99 0.336 0.353 0.966 5.16 10.876 41224 39.747
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.406 2.55 98.7 1.049 1.1 0.724 1.82 10.863
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 2h31 2.406 47.33 39161 2061 99.02 0.1796 0.177 0.1831 0.2293 0.2396 RANDOM 39.167
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] -0.19 2.78 -2.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.63 r_dihedral_angle_3_deg 16.315 r_dihedral_angle_4_deg 14.615 r_dihedral_angle_1_deg 6.27 r_angle_other_deg 2.328 r_angle_refined_deg 1.585 r_chiral_restr 0.072 r_bond_other_d 0.035 r_bond_refined_d 0.012 r_gen_planes_other 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.63 r_dihedral_angle_3_deg 16.315 r_dihedral_angle_4_deg 14.615 r_dihedral_angle_1_deg 6.27 r_angle_other_deg 2.328 r_angle_refined_deg 1.585 r_chiral_restr 0.072 r_bond_other_d 0.035 r_bond_refined_d 0.012 r_gen_planes_other 0.011 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6528 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 150
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing PDB_EXTRACT data extraction