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Crystal structure of rDcaUPO A161C mutant from Daldinia caldariorum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Daldinia caldariorum
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 279 10% (w/v) PEG 3350, 100 mM Imidazole/Hydrochloric acid, pH 6.5, 200 mM Ammonium sulfate, 30% (v/v) 2-Methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.05 40.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.558 α = 90 b = 107.52 β = 90 c = 120.016 γ = 90
Symmetry Space Group C 2 2 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 PILATUS3 6M 2022-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9779 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.47 61.27 99.8 0.999 22.3 11.8 81310
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 1.47 1.55 0.876
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.50000155539 40.0414080291 1.34757518298 77167 1899 99.9041959581 0.142880751083 0.142565893195 0.1453 0.155127258182 0.1575 21.3084746591
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 15.6231210063 f_angle_d 1.21016190635 f_chiral_restr 0.0491181895878 f_bond_d 0.00810666100707 f_plane_restr 0.00628106404882
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3481 Nucleic Acid Atoms Solvent Atoms 501 Heterogen Atoms 138
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing Coot model building