7ECT

Crystal Structure of Aspergillus terreus Glutamate Dehydrogenase (AtGDH) Complexed With Tartrate and NADPH


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5XVX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.32950.2 M Sodium tartrate dibasic, 20% PEG3350 pH 7.3
Crystal Properties
Matthews coefficientSolvent content
4.0369.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.86α = 90
b = 153.09β = 90
c = 259.27γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2018-08-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.939.2999.80.420.460.964.736.753084
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.931001.521.650.656.7

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 REPLACEMENTTHROUGHOUT5XVX2.939.2950428265599.850.224910.222540.26853RANDOM41.35
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]
-6.11-0.967.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.93
r_dihedral_angle_3_deg16.262
r_dihedral_angle_4_deg15.659
r_dihedral_angle_1_deg6.26
r_long_range_B_refined4.821
r_long_range_B_other4.821
r_mcangle_it3.213
r_mcangle_other3.213
r_scangle_other2.982
r_mcbond_it1.986
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.93
r_dihedral_angle_3_deg16.262
r_dihedral_angle_4_deg15.659
r_dihedral_angle_1_deg6.26
r_long_range_B_refined4.821
r_long_range_B_other4.821
r_mcangle_it3.213
r_mcangle_other3.213
r_scangle_other2.982
r_mcbond_it1.986
r_mcbond_other1.986
r_scbond_it1.767
r_scbond_other1.765
r_angle_refined_deg1.587
r_angle_other_deg0.989
r_chiral_restr0.078
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
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 Atoms10376
Nucleic Acid Atoms
Solvent Atoms87
Heterogen Atoms246

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing