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Crystal structure of GH19 domain of D29-LysA in complex with product (GlcNAc)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9HRM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 13% (v/v) MPD, 9% (v/v) PEG 1K, 9% PEG (w/v) 3350, 0.1 M buffer pH 6.1, and DL-amino-acids (glutamic acid, alanine, glycine; lysine, serine) at 20 mM
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.165 α = 90 b = 56.577 β = 90 c = 152.623 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 EIGER X 4M 2023-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
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 2.43 76.31 96.6 0.174 0.983 6.1 3.9 12304 33.78
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 2.43 2.52 97.9 0.891 0.516 4.1
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 2.43 76.31 1.34 12264 651 95.95 0.205 0.2022 0.2017 0.2562 0.2559 32.02
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 13.9788 f_angle_d 0.773 f_chiral_restr 0.0476 f_plane_restr 0.013 f_bond_d 0.0045
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2684 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 15
Software Software Software Name Purpose PHENIX refinement autoPROC data processing Aimless data scaling PHASER phasing