9YB6 | pdb_00009yb6

Human Mitochondrial Aspartate Aminotransferase complex with PLP at 1.5 Angstrom.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherIn lab model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2930.1 M Ammonium Sulfate, 0.05 M Sodium Acetate, 23% PEG-3350, pH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.2545.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.18α = 101.393
b = 59.168β = 101.722
c = 67.167γ = 95.408
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2025-04-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.9537Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.548.51596.80.9956.13.7129693
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.530.3610.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.548.515129693631596.7550.1870.18550.19410.20940.217317.241
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]
-0.119-0.545-0.6960.833-0.047-0.229
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg12.992
r_dihedral_angle_3_deg10.569
r_dihedral_angle_1_deg5.287
r_dihedral_angle_2_deg4.164
r_lrange_it3.791
r_lrange_other3.326
r_scangle_it0.929
r_scangle_other0.929
r_angle_refined_deg0.896
r_mcangle_it0.863
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg12.992
r_dihedral_angle_3_deg10.569
r_dihedral_angle_1_deg5.287
r_dihedral_angle_2_deg4.164
r_lrange_it3.791
r_lrange_other3.326
r_scangle_it0.929
r_scangle_other0.929
r_angle_refined_deg0.896
r_mcangle_it0.863
r_mcangle_other0.863
r_scbond_it0.528
r_scbond_other0.528
r_mcbond_it0.476
r_mcbond_other0.476
r_angle_other_deg0.358
r_nbd_refined0.195
r_symmetry_nbd_other0.191
r_nbtor_refined0.175
r_nbd_other0.157
r_xyhbond_nbd_refined0.079
r_symmetry_nbd_refined0.077
r_symmetry_nbtor_other0.073
r_symmetry_xyhbond_nbd_refined0.061
r_chiral_restr0.048
r_bond_other_d0.003
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6324
Nucleic Acid Atoms
Solvent Atoms994
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing