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Structure of an acyltransferase involved in mannosylerythritol lipid formation from Pseudozyma tsukubaensis in type B crystal
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other A model determined by SAD method
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 1.99 38.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.911 α = 90 b = 71.911 β = 90 c = 128.648 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 2021-11-29 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 1.59 47.96 99.8 0.05 0.054000000000000006 0.02 1 18.75 7.4 68145 27.15
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 1.59 1.68 1.334 1.431 0.648
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 1.59 47.94 1.34 68133 3407 99.82 0.1889 0.1876 0.1883 0.2135 0.2131 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 7.476 f_angle_d 0.969 f_chiral_restr 0.062 f_plane_restr 0.01 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4258 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 21
Software Software Software Name Purpose PHENIX refinement XDS data scaling XDS data reduction PHASER phasing