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LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase in complex with coenzyme A
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 5 ul 28 mg/ml LarE (100 mM Tris-HCl pH 7.5, 300 mM NaCl) containing 0.9 mM coenzyme A were mixed with 5 ul of reservoir solution. Hanging drop reservoir contained 100 ul of 30.0% v/v pentaerythritol ethoxylate (15/4 EO/OH), 50 mM BIS-TRIS pH 6.5, 100 mM ammonium sulfate.
Crystal Properties Matthews coefficient Solvent content 2.42 49.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.362 α = 90 b = 107.362 β = 90 c = 319.849 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 2016-07-31 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 2.09 47.95 99.7 0.091 0.1 0.04 0.998 14.7 6.1 111492 33.46
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 2.09 2.12 97.1 0.99 1.083 0.433 0.509 6
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 2.088 47.746 1.91 211427 10496 99.63 0.1966 0.1946 0.199 0.2335 0.2378 43.7285
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 4.993 f_angle_d 0.951 f_chiral_restr 0.055 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11607 Nucleic Acid Atoms Solvent Atoms 605 Heterogen Atoms 318
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction