9AYI | pdb_00009ayi

Human malic enzyme 2 cofactor complex at 1.89 Angstrom.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8W24 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72910.1 M Bis-Tris, 0.1 M Ammonium Tartrate, 0.02 M Potassium Citrate, 20% PEG-3350.
Crystal Properties
Matthews coefficientSolvent content
2.6753.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.325α = 65.32
b = 98.166β = 70.75
c = 107.739γ = 74.89
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2023-07-07MSINGLE 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
11.8947.4298.20.996.93.6200119
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)
11.891.9379.90.4831.63.5

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 REPLACEMENTTHROUGHOUT1.8947.421898401025697.120.178360.177120.1850.200960.2067RANDOM29.068
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]
0.761.56-1.51-0.49-0.36-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.727
r_dihedral_angle_1_deg5.792
r_long_range_B_refined5.17
r_long_range_B_other4.982
r_dihedral_angle_2_deg4.562
r_scangle_other3.036
r_mcangle_it2.294
r_mcangle_other2.294
r_scbond_it1.791
r_scbond_other1.791
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.727
r_dihedral_angle_1_deg5.792
r_long_range_B_refined5.17
r_long_range_B_other4.982
r_dihedral_angle_2_deg4.562
r_scangle_other3.036
r_mcangle_it2.294
r_mcangle_other2.294
r_scbond_it1.791
r_scbond_other1.791
r_mcbond_it1.391
r_mcbond_other1.391
r_angle_refined_deg1.094
r_angle_other_deg0.404
r_chiral_restr0.056
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms17334
Nucleic Acid Atoms
Solvent Atoms1960
Heterogen Atoms418

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing