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Crystal structure of Medicago truncatula glutamate dehydrogenase 2 in complex with 3-(1H-Tetrazol-5-yl)benzoic acid and NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8S38
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 292 60mM Divalents (MgCl2, CaCl2)
0.1M Tris (base)/;Bicine pH 8.5
20% v/v PEG 500* MME; 10 % w/v PEG 20000, 10% etylene glycol
Crystal Properties Matthews coefficient Solvent content 2.97 58.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.809 α = 78.998 b = 109.861 β = 78.482 c = 156.366 γ = 72.219
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 PILATUS 6M-F 2021-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.3 75.86 91 0.073 0.103 0.997 8.7 1.99 230242 33.63
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.4 62.5 0.43 0.43 0.72 2.1 1.93
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 2.3 65.69 1.95 230164 1151 84.01 0.1686 0.1685 0.1695 0.188 0.1906 48.34
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 17.1841 f_angle_d 0.976 f_chiral_restr 0.0617 f_bond_d 0.0081 f_plane_restr 0.0066
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 38008 Nucleic Acid Atoms Solvent Atoms 1208 Heterogen Atoms 350
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing