5XVX

Crystal Structure of Aspergillus niger Glutamate Dehydrogenase Complexed With Alpha-ketoglutarate and NADPH


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52950.1 M sodium citrate (pH 5.5), 20% (w/v) PEG 3000
Crystal Properties
Matthews coefficientSolvent content
7.1282.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 174.46α = 90
b = 174.46β = 90
c = 240.43γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2014-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.9763ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.83599.60.0920.9917.0812.2128967
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.997.90.410.965.110.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.834122517644899.650.135820.135180.14799RANDOM29.177
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]
0.210.110.21-0.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.899
r_dihedral_angle_4_deg16.9
r_dihedral_angle_3_deg11.931
r_long_range_B_refined9.045
r_long_range_B_other7.673
r_dihedral_angle_1_deg5.98
r_scangle_other3.932
r_scbond_it2.661
r_scbond_other2.654
r_mcangle_other2.235
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.899
r_dihedral_angle_4_deg16.9
r_dihedral_angle_3_deg11.931
r_long_range_B_refined9.045
r_long_range_B_other7.673
r_dihedral_angle_1_deg5.98
r_scangle_other3.932
r_scbond_it2.661
r_scbond_other2.654
r_mcangle_other2.235
r_mcangle_it2.233
r_mcbond_it1.667
r_mcbond_other1.661
r_angle_refined_deg1.654
r_angle_other_deg0.979
r_chiral_restr0.101
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.006
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3473
Nucleic Acid Atoms
Solvent Atoms674
Heterogen Atoms210

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing