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S127A variant of LarB, a carboxylase/hydrolase involved in synthesis of the cofactor for lactate racemase, in complex with authentic substrate NaAD and soaked with CS2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7MJ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 100 mM magnesium formate, 20% w/v PEG 3350, 2 mM nitrilotriacetic acid neutralized to a pH of ~7.5 with sodium hydroxide, and 0.7 mM zinc sulfate, 10 mM EDTA, 10 mM Nicotinic acid adenine dinucleotide sodium salt, soaked with ~10-15% Carbon disulfide for 20 minutes during freezing
Crystal Properties Matthews coefficient Solvent content 2.38 48.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.839 α = 90 b = 118.839 β = 90 c = 211.289 γ = 90
Symmetry Space Group P 4 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 PIXEL DECTRIS EIGER X 9M 2022-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.5498 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.65 84.03 100 0.983 6.5 6.7 44856
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.75 0.38 1.1
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.65 78.96 1.34 44538 2245 99.44 0.2434 0.2418 0.244 0.2728 0.2786
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 13.588 f_angle_d 1.002 f_chiral_restr 0.051 f_bond_d 0.018 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8360 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 219
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction Aimless data scaling PHASER phasing