7ECS

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72952.4 M Na malonate pH 7.0
Crystal Properties
Matthews coefficientSolvent content
4.0569.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.15α = 90
b = 153.74β = 90
c = 259.88γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2016-07-09MSINGLE 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
11.7439.3999.90.10.110.9916.727.2244015
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)
11.741.8499.10.830.90.762.396.53

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 REPLACEMENTTHROUGHOUT5XVX1.7439.382318261220299.840.140430.139240.16299RANDOM20.459
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]
-1.410.361.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.773
r_dihedral_angle_4_deg16.352
r_dihedral_angle_3_deg12.172
r_dihedral_angle_1_deg5.942
r_long_range_B_refined5.926
r_long_range_B_other5.765
r_scangle_other4.604
r_scbond_it3.287
r_scbond_other3.287
r_mcangle_it2.329
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.773
r_dihedral_angle_4_deg16.352
r_dihedral_angle_3_deg12.172
r_dihedral_angle_1_deg5.942
r_long_range_B_refined5.926
r_long_range_B_other5.765
r_scangle_other4.604
r_scbond_it3.287
r_scbond_other3.287
r_mcangle_it2.329
r_mcangle_other2.329
r_angle_refined_deg2.281
r_mcbond_it1.882
r_mcbond_other1.882
r_angle_other_deg1.154
r_chiral_restr0.147
r_bond_refined_d0.025
r_gen_planes_refined0.013
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 Atoms10401
Nucleic Acid Atoms
Solvent Atoms1742
Heterogen Atoms330

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing