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A broad-substrate spectrum lactate racemase A from Isosphaera pallida in complex with D-2-Hydroxyisovalerate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9EIA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 294 0.1 M Imidazole/MES monohydrate, pH 6.5, 20 % PEG 500 MME, 20% PEG 20,000, and 120 mM each of monosaccharides (D-Glucose, D-Mannose, D-Galactose, L-Fucose, D-Xylose and N-Acetyl-D-Glucosamine), and 3 mM D-2-hydroxyisovaleric acid (pH adjusted with 95 mM NaOH, pH ~7-8)
Crystal Properties Matthews coefficient Solvent content 2.23 44.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.024 α = 90 b = 45.246 β = 91.06 c = 118.218 γ = 90
Symmetry Space Group P 1 21 1
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 16M 2024-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97934 NSLS-II 17-ID-2
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 1.65 29.71 99.1 0.118 0.127 0.048 0.998 10.9 6.9 100330
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 1.65 1.68 93.4 0.716 0.774 0.291 0.762 2.6
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 FREE R-VALUE 1.65 29.71 1.34 100303 10039 98.96 0.1673 0.166 0.1609 0.191 0.1869
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 14.891 f_angle_d 1.015 f_chiral_restr 0.067 f_bond_d 0.007 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6342 Nucleic Acid Atoms Solvent Atoms 635 Heterogen Atoms 90
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing