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Crystal structure of Chaetomium thermophilum Naa20 in complex with a bisubstrate analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5K18
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 CtNaa20 was concentrated to 20 mg/ml and mixed in a 1:3 molar ratio with CoA-Ac-MDEL. The crystallization drops contained 200 nl protein solution and 200 nl precipitant solution (15 % (v/v) propanol, 0.2 M ammonium acetate and 0.1 M TRIS pH 8.5).
Crystal Properties Matthews coefficient Solvent content 2.72 54.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.15 α = 90 b = 114.453 β = 90.19 c = 47.416 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 100 PIXEL DECTRIS EIGER X 16M 2020-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.976247 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.57 47.42 98.7 0.087 0.056 0.998 8.6 6.6 67562 20.51
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.57 1.6 98.4 1.306 0.817 0.605 6.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5k18 1.57 47.42 1.36 65018 3321 94.96 0.1731 0.1713 0.1724 0.2053 0.2072 30.9085
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3128 Nucleic Acid Atoms Solvent Atoms 577 Heterogen Atoms 296
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing