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Crystal structure of rMcL-1 in complex with N-acetyl-D-galactosamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8VCK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291.15 0.2 M potassium thiocyanate, 0.1 M Bis Tris propane, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.37 48.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.951 α = 90 b = 64.157 β = 115.68 c = 75.694 γ = 90
Symmetry Space Group I 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 101 PIXEL DECTRIS PILATUS 200K 2023-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.66 46.22 99.6 0.046 23.3 7.3 37624 12.28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.66 1.69 0.564
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 1.66 34.11 1.34 37619 1879 99.61 0.1523 0.1507 0.1505 0.1818 0.1808 14.58
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 13.7094 f_angle_d 1.3584 f_chiral_restr 0.0982 f_plane_restr 0.0197 f_bond_d 0.0152
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2399 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 143
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing