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The structure of the glycopeptidase catalytic domain including the linker of Amuc_1438
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.2M (NH4)2PO4, 20% (W/V) peg3350, and 0,1M bicine, pH 9.0
Crystal Properties Matthews coefficient Solvent content 2.71 54.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.233 α = 90 b = 91.471 β = 90 c = 161.674 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 100 PIXEL DECTRIS PILATUS 200K 2020-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-002 1.54187
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.5 25 98.7 0.043 15.2 4.1 36634 38.53
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 0.195
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 2.5 24.92 1.34 36381 1827 98.02 0.2342 0.2317 0.2313 0.2831 0.2825 37.27
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 3.8664 f_angle_d 0.4493 f_chiral_restr 0.0396 f_plane_restr 0.0036 f_bond_d 0.0018
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6553 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 7
Software Software Software Name Purpose PHENIX refinement SHARP phasing