6DNB

Crystal structure of T110A:S256A mutant human Glutamate oxaloacetate transaminase 1 (GOT1)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3II0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2980.1 M Tris pH 8.5, 20% w/v/ PEG MME 2,000, 0.2 M Trimethylamine N-oxide dehydrate
Crystal Properties
Matthews coefficientSolvent content
2.3247.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.085α = 90
b = 84.085β = 90
c = 210.128γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2017-04-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.9787APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.75099.760.0847.6214.2446568
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.740.51

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 REPLACEMENTTHROUGHOUT3ii01.75046568246499.760.181450.1790.22873RANDOM24.887
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.829
r_dihedral_angle_4_deg18.733
r_dihedral_angle_3_deg14.919
r_long_range_B_other7.046
r_long_range_B_refined7.044
r_dihedral_angle_1_deg6.505
r_scangle_other5.416
r_scbond_it3.728
r_scbond_other3.702
r_mcangle_other3.232
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.829
r_dihedral_angle_4_deg18.733
r_dihedral_angle_3_deg14.919
r_long_range_B_other7.046
r_long_range_B_refined7.044
r_dihedral_angle_1_deg6.505
r_scangle_other5.416
r_scbond_it3.728
r_scbond_other3.702
r_mcangle_other3.232
r_mcangle_it3.23
r_mcbond_it2.367
r_mcbond_other2.346
r_angle_refined_deg2.167
r_angle_other_deg1.202
r_chiral_restr0.165
r_bond_refined_d0.022
r_gen_planes_refined0.011
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 Atoms3243
Nucleic Acid Atoms
Solvent Atoms237
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing