5XVI | pdb_00005xvi

Crystal Structure of Aspergillus niger Apo- Glutamate Dehydrogenase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3SBO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529520% PEG 3350, 0.1 M NaCl, 0.1 M Tris-Cl, pH 8.5, 0.01 M BaCl2
Crystal Properties
Matthews coefficientSolvent content
2.6653.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.8α = 103.46
b = 92.82β = 94.17
c = 111.69γ = 120.13
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2013-08-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

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
12.840920.060.9911.2269072
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)
12.82.9860.280.843.61.6

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3SBO2.83565578345191.780.229870.225710.230.310110.31RANDOM27.449
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]
-3.46-1.40.94-2.291.435.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.523
r_dihedral_angle_3_deg17.868
r_dihedral_angle_4_deg15.882
r_dihedral_angle_1_deg6.879
r_long_range_B_refined3.608
r_long_range_B_other3.604
r_angle_other_deg2.083
r_mcangle_it1.981
r_mcangle_other1.981
r_scangle_other1.578
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.523
r_dihedral_angle_3_deg17.868
r_dihedral_angle_4_deg15.882
r_dihedral_angle_1_deg6.879
r_long_range_B_refined3.608
r_long_range_B_other3.604
r_angle_other_deg2.083
r_mcangle_it1.981
r_mcangle_other1.981
r_scangle_other1.578
r_angle_refined_deg1.429
r_mcbond_it1.156
r_mcbond_other1.156
r_scbond_it0.891
r_scbond_other0.891
r_chiral_restr0.075
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_gen_planes_other0.003
r_bond_other_d0.002
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 Atoms20813
Nucleic Acid Atoms
Solvent Atoms585
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing