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Crystal structure of the human glutamate dehydrogenase 2 (hGDH2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L1F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 PEG 8000, MPD, NaCl, sodium phosphate
Crystal Properties Matthews coefficient Solvent content 2.99 58.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.795 α = 90 b = 149.304 β = 90 c = 433.315 γ = 90
Symmetry Space Group C 2 2 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 2016-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.93 48.15 98.9 0.214 13.9 13.6 83838 55.5027904224
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.93 3.09 92.6 12.7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1L1F 2.93428699014 47.6510455293 1.89429104804 160982 8056 98.5835451177 0.195747385819 0.192935363307 0.248811017326 0.1888 52.3493357802
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 1.72304611035 f_angle_d 0.387069077385 f_chiral_restr 0.0391925073968 f_plane_restr 0.00348148519433 f_bond_d 0.00164080845126
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22381 Nucleic Acid Atoms Solvent Atoms 1624 Heterogen Atoms 155
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XDS data scaling PHASER phasing