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Structure of an acyltransferase involved in mannosylerythritol lipid formation from Pseudozyma tsukubaensis in type A crystal
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other A model determined by SAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 21% PEG 3350, 300mM lithium chloride
Crystal Properties Matthews coefficient Solvent content 2.3 46.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.043 α = 90 b = 83.073 β = 90 c = 131.035 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 16M 2021-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 1.45 44.73 99.8 0.075 0.081 0.03 0.9990000000000001 15.68 7.4 103745 17.53
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.53 99.2 1.177 1.262 0.7290000000000001 2.29
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.45 35.08 1.35 103733 5187 99.79 0.172 0.1708 0.17 0.1943 0.1944 0
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 10.541 f_angle_d 0.897 f_chiral_restr 0.081 f_plane_restr 0.009 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4242 Nucleic Acid Atoms Solvent Atoms 702 Heterogen Atoms 16
Software Software Software Name Purpose PHENIX refinement XDS data scaling XDS data reduction PHASER phasing