5MPR | pdb_00005mpr

Single Amino Acid Variant of Human Mitochondrial Branched Chain Amino Acid Aminotransferase 2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION6.52930.2 M Sodiumfluoride, 0.1 M Bis Tris propane pH 6.5, 20% w/v Polyethylene glycol 3350
Crystal Properties
Matthews coefficientSolvent content
2.5952.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.032α = 90
b = 84.032β = 90
c = 105.446γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2016-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.62899.711.89.757390

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 DIFFRACTIONTHROUGHOUT1.627.5254393291299.660.130520.12790.140.179390.19RANDOM28.859
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]
0.20.20.2-0.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.82
r_sphericity_free29.486
r_sphericity_bonded17.965
r_dihedral_angle_4_deg16.156
r_dihedral_angle_3_deg13.275
r_scangle_other8.025
r_long_range_B_refined7.228
r_long_range_B_other7.228
r_scbond_it6.817
r_scbond_other6.816
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.82
r_sphericity_free29.486
r_sphericity_bonded17.965
r_dihedral_angle_4_deg16.156
r_dihedral_angle_3_deg13.275
r_scangle_other8.025
r_long_range_B_refined7.228
r_long_range_B_other7.228
r_scbond_it6.817
r_scbond_other6.816
r_rigid_bond_restr6.298
r_dihedral_angle_1_deg5.926
r_mcangle_other5.305
r_mcangle_it5.298
r_mcbond_it4.513
r_mcbond_other4.497
r_angle_refined_deg1.816
r_angle_other_deg0.875
r_chiral_restr0.116
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_gen_planes_other0.003
r_bond_other_d0.001
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2901
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing