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Room temperature X-ray crystallographic structure of a Jonesia denitrificans lytic polysaccharide monooxygenase at 1.1 angstrom resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AA7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Purified enzyme was incubated with a threefold molar excess of CuSO4 for 30 min at room temperature. To remove excess copper, the protein was loaded onto a desalting column equilibrated with 20 mM Tris-HCl pH 8.0. 30 ul protein solution at 48 mg/ml was mixed with 30 ul reservoir buffer consisting of 1.9 M DL-malic acid pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.34 47.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.04 α = 90 b = 75.56 β = 90 c = 120.36 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 295 CMOS RDI CMOS_8M 2015-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.000 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.1 32 97.3 13.7 10.7 1248110
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.16 95 10.4
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 5AA7 1.1 32 1.33 116060 2000 97.1 0.114 0.114 0.1146 0.128 0.1291
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 16.245 f_angle_d 0.975 f_chiral_restr 0.079 f_bond_d 0.008 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2188 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing