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Crystal structure of a SnoaL-like domain-containing protein from Mycobacterium ulcerans (Zinc Bound)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9PL2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 291 12% 4000, 0.1M sodium acetate pH 4.2, 10mM dihdrogen potassium phosphate. MyulA.17060.a.A1.PB00143 at 15 mg/mL. Liu-S-182 drop CD/4, Puck: PSL-0405, Cryo: 32% PEG 4000, 0.2M sodium acetate pH 4.0
Crystal Properties Matthews coefficient Solvent content 1.85 33.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.071 α = 90 b = 71.662 β = 90 c = 56.341 γ = 90
Symmetry Space Group C 2 2 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 EIGER2 XE 9M 2025-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9786 NSLS-II 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.31 46.92 92 0.043 0.045 0.012 1 26.4 12.6 53640
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.31 1.34 56.7 1.01 1.079 0.367 0.757 8.1
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 1.31 36.05 1.34 53640 2761 91.9 0.1503 0.1491 0.1634 0.1742 0.1846
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 14.751 f_angle_d 1.039 f_chiral_restr 0.081 f_plane_restr 0.012 f_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 988 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 9
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction