7ECR

Crystal Structure of Aspergillus terreus Glutamate Dehydrogenase (AtGDH) Complexed With Succinate and ADP-ribose


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72950.8 M Succinic acid, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
4.0669.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.88α = 90
b = 153.75β = 90
c = 259.95γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2016-07-06MSINGLE 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
11.7338.6899.20.110.110.9915.387.11246054
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)
11.731.8394.70.910.10.722.15.93

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 REPLACEMENTTHROUGHOUT5XVX1.7338.682337511230399.660.146160.1450.167RANDOM19.827
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]
-1.350.11.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.531
r_dihedral_angle_4_deg15.603
r_dihedral_angle_3_deg12.162
r_dihedral_angle_1_deg5.928
r_long_range_B_refined5.239
r_long_range_B_other5.239
r_scangle_other4.285
r_scbond_it3.034
r_scbond_other3.029
r_mcangle_it2.182
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.531
r_dihedral_angle_4_deg15.603
r_dihedral_angle_3_deg12.162
r_dihedral_angle_1_deg5.928
r_long_range_B_refined5.239
r_long_range_B_other5.239
r_scangle_other4.285
r_scbond_it3.034
r_scbond_other3.029
r_mcangle_it2.182
r_mcangle_other2.182
r_angle_refined_deg2.12
r_mcbond_it1.756
r_mcbond_other1.755
r_angle_other_deg1.101
r_chiral_restr0.137
r_bond_refined_d0.023
r_gen_planes_refined0.012
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 Atoms1476
Heterogen Atoms264

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing