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Structure of human Archease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YZ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 protein: 1966 uM in 25 mM HEPES pH 7.5, 100mM NaCl, 5 % glycerol, 1mM TCEP
reservoir: 0.2 M ammonium chloride, 20% w/v PEG 3350
drop composition: 200 nl reservoir + 200 nl protein
Crystal Properties Matthews coefficient Solvent content 2.47 50.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.981 α = 90 b = 79.981 β = 90 c = 65.164 γ = 90
Symmetry Space Group P 42 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 EIGER2 X 16M Toroidal mirror 2021-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9737 ESRF ID23-1
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 1.84 79.98 100 0.068 0.013 0.999 23.7 27.5 18949 49.91
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.84 1.88 100 0.743 0.471 25.1
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 FREE R-VALUE 5YZ1 1.84 39.99 1.34 18925 942 99.97 0.195 0.1937 0.1944 0.2212 0.2195 58.33
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.1023 f_angle_d 0.8407 f_chiral_restr 0.0528 f_plane_restr 0.0077 f_bond_d 0.0066
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1300 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement