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Chitin-active AA10 LPMO (GbpA) complexed with Cu(II) from Vibrio campbellii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Alphafold2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292.15 1.0M Ammonium sulfate, 0.1M ADA buffer, pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.36 66.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.433 α = 90 b = 113.433 β = 90 c = 213.761 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 CCD RAYONIX MX-300 2022-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 0.99984 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.44 30 99 0.125 0.127 0.024 29.1 26.2 52161 52.35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.44 2.48 84.1 1.19 1.31 0.518 0.454 0.72
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 Alphafold2 2.44 29.78 1.34 52042 2598 99 0.2063 0.2045 0.2049 0.2397 0.2398 73.82
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 11.1322 f_angle_d 0.4706 f_chiral_restr 0.0423 f_plane_restr 0.0039 f_bond_d 0.0019
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6408 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 7
Software Software Software Name Purpose PHENIX refinement Blu-Ice data collection HKL-2000 data scaling PHENIX model building PHENIX phasing XDS data reduction