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Crystal structure of Glutamate dehydrogenase from Burkholderia thailandensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AOE PDB entry 3aoe, search with two domains
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 Microlytics MCSG1 screen F1: 20% PEG 5000MME, 100mM BisTris pH 6.5; ButhA.17991.a.A1.PW33475 at 20mg/ml with 2.5mM NAD and 2.5mM Glu; cryo: 20% EG; tray 257704f1, puck smx9-3
Crystal Properties Matthews coefficient Solvent content 2.3 46.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.49 α = 90 b = 93.52 β = 106.23 c = 158.37 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 CCD RIGAKU SATURN 944+ 2014-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 50 96.7 0.083 0.09 14.91 6.6 174736 -3 22.28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 92.6 0.392 0.443 3.3 4.6
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 3aoe, search with two domains 2 45.842 1.34 174723 1995 96.75 0.1766 0.1761 0.1769 0.2222 0.2226 Random selection 30.5192
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 13.899 f_angle_d 1.033 f_chiral_restr 0.039 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18661 Nucleic Acid Atoms Solvent Atoms 1643 Heterogen Atoms 348
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing ARP model building Coot model building PHENIX refinement PDB_EXTRACT data extraction