5XWC

Crystal Structure of Aspergillus niger Glutamate Dehydrogenase Complexed With Alpha-iminoglutarate, 2-amino-2-hydroxyglutarate and NADP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529540% v/v PEG 300, 0.1M sodium cacodylate, pH 6.5, 0.2 M calcium acetate hydrate

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 173.41α = 90
b = 173.41β = 90
c = 241.83γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2016-05-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.9537ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.7535990.1113.47.9138857
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.8599.90.691.97.9

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 REPLACEMENTTHROUGHOUT1.7534131488692098.950.156130.155450.16921RANDOM28.291
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]
0.080.040.08-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.459
r_dihedral_angle_4_deg16.218
r_dihedral_angle_3_deg11.976
r_long_range_B_refined7.923
r_long_range_B_other7.227
r_dihedral_angle_1_deg5.822
r_scangle_other3.928
r_scbond_it2.628
r_scbond_other2.628
r_mcangle_other1.957
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.459
r_dihedral_angle_4_deg16.218
r_dihedral_angle_3_deg11.976
r_long_range_B_refined7.923
r_long_range_B_other7.227
r_dihedral_angle_1_deg5.822
r_scangle_other3.928
r_scbond_it2.628
r_scbond_other2.628
r_mcangle_other1.957
r_mcangle_it1.956
r_angle_refined_deg1.654
r_mcbond_it1.366
r_mcbond_other1.362
r_angle_other_deg0.992
r_chiral_restr0.201
r_bond_refined_d0.012
r_bond_other_d0.008
r_gen_planes_refined0.007
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 Atoms3469
Nucleic Acid Atoms
Solvent Atoms527
Heterogen Atoms370

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing