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Crystal Structure of endo-beta-N-acetylglucosaminidase from Cordyceps militaris D154N/E156Q mutant in complex with fucosyl-N-acetylglucosamine-Asn
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.6 277.15 0.1 M CHES-NaOH (pH 8.6) and 20 % PEG3350
Crystal Properties Matthews coefficient Solvent content 3.02 59.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.912 α = 90 b = 105.912 β = 90 c = 62.217 γ = 120
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 PILATUS3 S 2M 2018-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.35 50 99 0.134 0.974 9.8 4.7 16268
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.39 95.1 0.554 0.787 1.7 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.36 45.9 15471 792 99.01 0.1877 0.1851 0.1835 0.2357 0.2273 RANDOM 60.795
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] 0.04 0.02 0.04 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.077 r_dihedral_angle_4_deg 16.968 r_dihedral_angle_3_deg 14.963 r_dihedral_angle_1_deg 6.916 r_angle_refined_deg 1.494 r_angle_other_deg 1.265 r_chiral_restr 0.059 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.077 r_dihedral_angle_4_deg 16.968 r_dihedral_angle_3_deg 14.963 r_dihedral_angle_1_deg 6.916 r_angle_refined_deg 1.494 r_angle_other_deg 1.265 r_chiral_restr 0.059 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2274 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHENIX phasing