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F195L/I200F/M298L Streptomyces coelicolor Laccase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8U8P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 296 Crystals were prepared using hanging drop vapor-diffusion technique at room temperature (~296 K). Protein is at a concentration of 18.5 mg/ml in 50 mM H3BO3, 0.1 M NaCl, pH 9.0 buffer. The well buffer contains 0.1 M glycine, 0.5 M NaCl, pH 9.0, and 37-40% (v/v) PEG (polyethylene glycol) monomethyl ether 550. 500 uL of well buffer is added to each well and protein is mixed with well buffer at a 1.5 uL:1.5 uL ratio. The crystal growth time was ca. 1 week.
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.832 α = 90 b = 177.832 β = 90 c = 177.832 γ = 90
Symmetry Space Group P 43 3 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 S 9M 2023-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.000006 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.64 79.53 99.96 0.2716 0.2751 0.998 16.58 39.5 28814 58.18
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.64 2.734 99.93 2.903 2.94 0.849 1.69 39.8
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 2.64 79.53 1.35 28806 2809 99.96 0.1867 0.1855 0.193 0.2077 0.2151 52.86
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 7.1942 f_angle_d 0.4769 f_chiral_restr 0.0452 f_plane_restr 0.0043 f_bond_d 0.0021
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2150 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 51
Software Software Software Name Purpose BOS data collection xia2 data scaling PHENIX phasing PHENIX refinement xia2 data reduction