5XW0

Crystal Structure of Aspergillus niger Glutamate Dehydrogenase Complexed With Isophthalate and NADPH


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62950.1 M MES (pH 6.0) 30% (v/v) PEG 200, 5 % (w/v) PEG 3000
Crystal Properties
Matthews coefficientSolvent content
7.0682.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 173.48α = 90
b = 173.48β = 90
c = 241.14γ = 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
11.97099.90.0540.9924.37.4109208
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)
11.9298.80.420.614.56.9

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 REPLACEMENTTHROUGHOUT1.940103738546099.90.168670.168050.18038RANDOM31.006
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]
0.170.080.17-0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.785
r_dihedral_angle_4_deg18.212
r_dihedral_angle_3_deg11.756
r_long_range_B_refined5.939
r_dihedral_angle_1_deg5.802
r_long_range_B_other5.66
r_scangle_other3.835
r_scbond_it2.422
r_scbond_other2.406
r_mcangle_other2.401
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.785
r_dihedral_angle_4_deg18.212
r_dihedral_angle_3_deg11.756
r_long_range_B_refined5.939
r_dihedral_angle_1_deg5.802
r_long_range_B_other5.66
r_scangle_other3.835
r_scbond_it2.422
r_scbond_other2.406
r_mcangle_other2.401
r_mcangle_it2.4
r_mcbond_it1.663
r_mcbond_other1.661
r_angle_refined_deg1.444
r_angle_other_deg0.95
r_chiral_restr0.086
r_bond_refined_d0.01
r_bond_other_d0.007
r_gen_planes_refined0.006
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 Atoms307
Heterogen Atoms166

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing