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X-ray crystal structure of N372D mutant of endo-1,4-beta glucanase from Eisenia fetida
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WC3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 18% PEG3350, 0.2 M magnesium chloride, 50 mM sodium acetate pH 5.0
Crystal Properties Matthews coefficient Solvent content 1.86 33.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.304 α = 90 b = 71.614 β = 113.821 c = 55.097 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER X 16M 2021-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.9800 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.6 50 99.5 0.086 0.998 10 3.5 49763 12.35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 96.6 0.491 0.873 2.7
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 1.6 48.76 1.335 49718 2467 99.4 0.1479 0.1466 0.1467 0.173 0.1729 15.09
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 11.52 f_angle_d 0.8318 f_chiral_restr 0.05064 f_plane_restr 0.005656 f_bond_d 0.005384
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3413 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms 9
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing