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Crystal structure of human Naa50 in complex with CoA and an inhibitor (compound 4a) identified using DNA encoded library technology
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OB0 unpublished model, solved using PDB entry 2Ob0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 294 Compound 4a soaked into crystals of Naa50+CoA. CoA co-crystals: Naa50 apo protein (14.3 mg/ml) was incubated with CoA in a 1:3 molar ratio on ice for 60 min. Crystallization solution: 0.1 M Na acetate, pH5.0, 25% (w/v) PEG 3350, 10 mM Dithiothreitol (DTT), and 0.1% Dioxane
Crystal Properties Matthews coefficient Solvent content 2.72 54.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.35 α = 90 b = 102.38 β = 106.92 c = 67.55 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 PIXEL DECTRIS PILATUS 6M 2018-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.87 64.63 91.3 0.054 0.998 11.9 3.3 38205 43.19
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 2.03 55.5 0.778 0.421 1.2 2.5
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(Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT unpublished model, solved using PDB entry 2Ob0 1.87 64.63 38205 1853 73.5 0.201 0.2 0.1957 0.222 0.2218 RANDOM 47.48
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] -0.5176 0.0201 0.4929 0.0247
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.05 t_omega_torsion 3.22 t_angle_deg 1.17 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.05 t_omega_torsion 3.22 t_angle_deg 1.17 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3698 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 330
Software Software Software Name Purpose XDS data reduction BUSTER refinement PDB_EXTRACT data extraction autoPROC data scaling BUSTER phasing