4KTV

Structural insights of MAT enzymes: MATa2b complexed with adenosine and pyrophosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PO2PDB ENTRIES 2PO2 AND 2YDY
experimental modelPDB 2YDYPDB ENTRIES 2PO2 AND 2YDY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.52980.1M MES/Imidazole pH 6.5 0.1M Carboxylic acids 20% Ethylene glycol 10% PEG 8K, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5451.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.09α = 90
b = 116.57β = 90
c = 299.48γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOCALBAXALOC

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
13.2150.03599.93.342893428512.22.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.23.37100

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRIES 2PO2 AND 2YDY3.3108.8738907194999.80.180.1760.2670.35
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]
6.50.88-7.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.344
r_dihedral_angle_3_deg18.246
r_dihedral_angle_4_deg16.086
r_dihedral_angle_1_deg7.069
r_angle_refined_deg1.265
r_angle_other_deg0.759
r_chiral_restr0.066
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.344
r_dihedral_angle_3_deg18.246
r_dihedral_angle_4_deg16.086
r_dihedral_angle_1_deg7.069
r_angle_refined_deg1.265
r_angle_other_deg0.759
r_chiral_restr0.066
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16362
Nucleic Acid Atoms
Solvent Atoms37
Heterogen Atoms101

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing
SCALAdata scaling