3AOE

Crystal structure of hetero-hexameric glutamate dehydrogenase from Thermus thermophilus (Leu bound form)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62930.1M sodium citrate tribasic (pH5.6), 1.0M ammonium phosphate monobasic, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.652.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.986α = 90
b = 146.093β = 90
c = 158.284γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 210mirrors2010-05-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0Photon FactoryAR-NW12A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.630.2299.987634876342.72.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.64100

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1B262.630.2283048438899.950.195940.192570.25961RANDOM44.615
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]
0.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.247
r_dihedral_angle_3_deg20.798
r_dihedral_angle_4_deg20.11
r_dihedral_angle_1_deg6.005
r_scangle_it3.307
r_scbond_it1.923
r_angle_refined_deg1.464
r_mcangle_it1.165
r_mcbond_it0.593
r_chiral_restr0.102
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.247
r_dihedral_angle_3_deg20.798
r_dihedral_angle_4_deg20.11
r_dihedral_angle_1_deg6.005
r_scangle_it3.307
r_scbond_it1.923
r_angle_refined_deg1.464
r_mcangle_it1.165
r_mcbond_it0.593
r_chiral_restr0.102
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms18973
Nucleic Acid Atoms
Solvent Atoms312
Heterogen Atoms54

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling