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LarB, a carboxylase/hydrolase involved in synthesis of the cofactor for lactate racemase, in complex with NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D7A
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 NAD+ (disodium salt)
Crystal Properties Matthews coefficient Solvent content 2.44 49.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.445 α = 90 b = 120.445 β = 90 c = 213.589 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 2019-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.305 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 3.4 41.762 93.8 0.992 7.6 4.5 20627
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 3.4 3.67 0.674
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 THROUGHOUT 1D7A 3.402 41.762 1.34 20551 983 92.02 0.2444 0.2432 0.2471 0.2689 0.27 110.678
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 15.356 f_angle_d 0.877 f_chiral_restr 0.051 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8226 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 92
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing