5XVV | pdb_00005xvv

Crystal Structure of Forward Inhibited Aspergillus niger Glutamate Dehydrogenase With Both Apo- and Alpha Ketoglutarate Bound Subunits


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2950.15 M potassium bromide, 20% w/v PEG 2000 MME
Crystal Properties
Matthews coefficientSolvent content
2.6152.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.26α = 103.4
b = 92.15β = 93.95
c = 111.06γ = 120.36
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2015-10-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
12.253595.50.0950.997.962135737
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)
12.252.35920.390.682.1

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.2533128936678695.530.160290.158260.170.198630.2RANDOM25.927
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]
-0.2-0.29-0.37-0.110.10.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.369
r_dihedral_angle_4_deg14.754
r_dihedral_angle_3_deg14.635
r_dihedral_angle_1_deg6.228
r_long_range_B_refined5.961
r_long_range_B_other5.953
r_scangle_other3.198
r_mcangle_it2.203
r_mcangle_other2.203
r_scbond_it2.036
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.369
r_dihedral_angle_4_deg14.754
r_dihedral_angle_3_deg14.635
r_dihedral_angle_1_deg6.228
r_long_range_B_refined5.961
r_long_range_B_other5.953
r_scangle_other3.198
r_mcangle_it2.203
r_mcangle_other2.203
r_scbond_it2.036
r_scbond_other2.036
r_angle_refined_deg1.433
r_mcbond_it1.355
r_mcbond_other1.355
r_angle_other_deg0.971
r_chiral_restr0.084
r_bond_refined_d0.011
r_bond_other_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.001
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 Atoms20806
Nucleic Acid Atoms
Solvent Atoms1516
Heterogen Atoms186

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing