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LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, in complex with iron
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UDQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294.15 4 ul ~39 mg/ml LarE (100 mM Tris-HCl pH 7.5, 300 mM NaCl) mixed with 4 ul of reservoir solution. Hanging drop reservoir contained 100 ul of 37.5% v/v pentaerythritol ethoxylate (15/4 EO/OH), 50 mM BIS-TRIS pH 6.5, 105 mM ammonium sulfate. Crystal soaked 4.5 minutes in 30.0% v/v pentaerythritol ethoxylate (15/4 EO/OH), 50 mM BIS-TRIS pH 5.5, 50 mM ammonium sulfate, 38 mM iron sulfate.
Crystal Properties Matthews coefficient Solvent content 2.42 49.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.546 α = 90 b = 107.546 β = 90 c = 318.289 γ = 90
Symmetry Space Group P 41 2 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 300 mm CCD 2016-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.9786 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.62 47.96 99.9 0.098 0.998 15.6 7.9 57095 55.12
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.62 2.69 99.3 0.812 0.684 8.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5UDQ 2.621 47.575 1.92 53433 5198 99.82 0.2127 0.2103 0.2149 0.259 0.2643 64.6372
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 13.529 f_angle_d 0.977 f_chiral_restr 0.053 f_bond_d 0.01 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11525 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 67
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing