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Sco GlgEI-V279S in complex with 4-alpha-glucoside of validamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4U31
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 289.15 0.2 mM Sodium citrate pH 7 and 10 % PEG 3,350
Crystal Properties Matthews coefficient Solvent content 3.19 62.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.049 α = 90 b = 113.049 β = 90 c = 311.506 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2020-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9787 APS 21-ID-F
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 1.75 55.78 96.21 0.09187 0.09576 0.02625 0.999 16.2 11.6 195923 23.59
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 1.75 1.813 71.7 1.308 1.618 0.9307 0.357 0.93 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4u31 1.75 55.78 1.33 195923 3734 94.01 0.1764 0.1762 0.1972 0.1943 26.4027
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 8.791 f_angle_d 0.889 f_chiral_restr 0.057 f_plane_restr 0.01 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10238 Nucleic Acid Atoms Solvent Atoms 1602 Heterogen Atoms 88
Software Software Software Name Purpose PHENIX refinement xia2 data scaling PDB_EXTRACT data extraction DIALS data reduction PHENIX phasing