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Crystal structure of Y281F mutant of Hyaluronate lyase B from Cutibacterium acnes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8FNX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291.15 0.1 M bis-tris pH 6.5, 0.4 M MgCl2, 16% PEG 3350, and 5 mM TCEP
Crystal Properties Matthews coefficient Solvent content 2.43 49.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.977 α = 91.95 b = 53.013 β = 98.03 c = 161.016 γ = 114.56
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2018-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.1 19.72 92.5 0.12 0.17 0.12 0.981 5.4 1.9 85175
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 2.1 2.21 0.548 0.775 0.548 0.853 1.8
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 2.1 19.72 16.43 85171 4357 92.61 0.271 0.2436 0.2457 0.2741 0.2743
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 4.434 f_angle_d 0.543 f_chiral_restr 0.041 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11563 Nucleic Acid Atoms Solvent Atoms 668 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement SCALA data scaling XDS data reduction PHASER phasing