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Crystal structure of an N-acetylgalactosamine deacetylase from F. plautii
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M CaCl2, 0.1 M MES pH 6.0, 18% PEG 4000, and 20 mM MnCl2
Crystal Properties Matthews coefficient Solvent content 1.67 26.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.584 α = 90 b = 69.186 β = 90 c = 104.325 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 PILATUS3 S 6M 2018-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9194 CLSI 08ID-1
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 1.6 46.2 97.7 0.02 1 27.4 22.9 48937
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 1.6 1.63 79.2 0.4 0.63 1.8 13.3
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 1.6 46.2 46465 2406 97.62 0.1402 0.1388 0.1537 0.1666 0.1787 RANDOM 19.049
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] 0.3 0.11 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.762 r_dihedral_angle_3_deg 12.675 r_dihedral_angle_4_deg 11.35 r_dihedral_angle_1_deg 7.242 r_angle_other_deg 3.812 r_mcangle_it 2.086 r_angle_refined_deg 1.942 r_mcbond_it 1.507 r_mcbond_other 1.506 r_chiral_restr 0.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.762 r_dihedral_angle_3_deg 12.675 r_dihedral_angle_4_deg 11.35 r_dihedral_angle_1_deg 7.242 r_angle_other_deg 3.812 r_mcangle_it 2.086 r_angle_refined_deg 1.942 r_mcbond_it 1.507 r_mcbond_other 1.506 r_chiral_restr 0.133 r_bond_refined_d 0.021 r_gen_planes_other 0.019 r_gen_planes_refined 0.012 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3070 Nucleic Acid Atoms Solvent Atoms 365 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling CRANK2 phasing