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Structure of the small subunit of the laccase-like Nlac protein from Pleurotus eryngii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold No special aspects
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 0.1 M Imidazole at pH 8.0 and 2.5 M NaCl
Crystal Properties Matthews coefficient Solvent content 3.11 60.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.72 α = 90 b = 124.72 β = 90 c = 55.812 γ = 90
Symmetry Space Group P 41 21 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 PILATUS 6M-F 2022-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979257 ALBA XALOC
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 1.6 47.16 99.9 0.999 14.29 26.2 58835 25.78
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 1.6 1.69 99.3 0.385 0.69
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.6 47.16 1.33 58713 1996 99.68 0.1949 0.1941 0.2191 0.1923 30.88
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 4.8441 f_angle_d 0.7796 f_chiral_restr 0.0453 f_bond_d 0.0059 f_plane_restr 0.0057
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2337 Nucleic Acid Atoms Solvent Atoms 315 Heterogen Atoms 25
Software Software Software Name Purpose PHENIX refinement PHENIX refinement autoPROC data reduction XDS data scaling PHASER phasing