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Crystal structure of Medicago truncatula glutamate dehydrogenase 2 in complex with 2-amino-2-hydroxyglutarate (reaction intermediate) and NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8S38 model of the same protein with different ligand
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1M Amino acids (0.02M DL-Glutamic acid monohydrate; 0.02M DL-Alanine; 0.02M Glycine; 0.02M DL-Lysine monohydrochloride; 0.02M DL-Serine )
0.1M Imidazole/MES monohydrate pH 6.5
20% v/v PEG 500* MME; 10 % w/v PEG 20000
Crystal Properties Matthews coefficient Solvent content 2.65 53.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.832 α = 90 b = 155.707 β = 90 c = 163.089 γ = 90
Symmetry Space Group P 21 21 21
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 2021-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9762 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.65 65.89 99.5 0.092 0.994 6.83 7.49 337626 20.18
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.75 98.7 1.445 1.548 0.532 1.11 7.56
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 65.89 1.35 337564 3376 99.5 0.1471 0.1468 0.1582 0.1735 0.1801 24.8
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 17.4799 f_angle_d 1.1525 f_chiral_restr 0.0647 f_bond_d 0.0118 f_plane_restr 0.0085
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18834 Nucleic Acid Atoms Solvent Atoms 2636 Heterogen Atoms 616
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing