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Neutron crystallographic structure of a Jonesia denitrificans lytic polysaccharide monooxygenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VG0
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. 14 ul protein solution at 48 mg/ml was mixed with 14 ul reservoir buffer consisting of 1.9 M DL-malic acid pH 7.0
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.5 α = 90 b = 76.4 β = 90 c = 122.1 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 neutron 295 AREA DETECTOR ORNL ANGER CAMERA 2015-05-21 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SPALLATION SOURCE ORNL Spallation Neutron Source BEAMLINE MANDI 2-4 ORNL Spallation Neutron Source MANDI
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 2.1 12 76 9.4 4.5 13989
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 2.1 2.17 59.4 2.7 2.5
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-Free (Depositor) Mean Isotropic B NEUTRON DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5VG0 2.1 12 2.38 13989 686 76 0.191 0.187 0.265
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 11.89 f_angle_d 0.56 f_chiral_restr 0.04 f_bond_d 0.002 f_plane_restr 0.002
Software Software Software Name Purpose PHENIX refinement PHENIX phasing Mantid data reduction