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Crystal Structure of GH19 domain of D29-LysA (Form III)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 9% MPD, 9% PEG 1K, 9% PEG 3350, 0.1 M buffer pH 6.1, and DL-amino-acids (glutamic acid, alanine, glycine; lysine, serine) at 20 mM
Crystal Properties Matthews coefficient Solvent content 1.85 33.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.048 α = 90 b = 57.04 β = 90 c = 151.305 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) Rpim 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 2.04 57.04 98.5 0.121 0.979 5.5 3.9 20836 22.74
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.1 99.6 0.558 0.514
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 2.04 53.37 1.34 20789 1040 97.95 0.1807 0.1778 0.1776 0.2349 0.2346 22.11
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 12.4976 f_angle_d 0.7736 f_chiral_restr 0.0469 f_plane_restr 0.0093 f_bond_d 0.0067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2681 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement autoPROC data processing Aimless data scaling PHASER phasing