5A19

The structure of MAT2A in complex with PPNP.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2P02PDB ENTRY 2P02

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.1 M HEPES PH 7.5, 30 % PEG 600
Crystal Properties
Matthews coefficientSolvent content
239

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.22α = 90
b = 95.49β = 90
c = 117.7γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2MMIRRORS2014-08-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-1DiamondI04-1

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
12.3374.0499.90.1320.71316225
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)
12.342.499.90.61.713.7

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2P022.3457.711530180599.80.165490.163440.20446RANDOM28.141
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]
0.05-0.060.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.62
r_dihedral_angle_4_deg21.248
r_dihedral_angle_3_deg12.797
r_dihedral_angle_1_deg6.406
r_long_range_B_refined3.591
r_long_range_B_other3.349
r_mcangle_it1.726
r_mcangle_other1.725
r_scangle_other1.674
r_angle_refined_deg1.276
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.62
r_dihedral_angle_4_deg21.248
r_dihedral_angle_3_deg12.797
r_dihedral_angle_1_deg6.406
r_long_range_B_refined3.591
r_long_range_B_other3.349
r_mcangle_it1.726
r_mcangle_other1.725
r_scangle_other1.674
r_angle_refined_deg1.276
r_mcbond_it1.04
r_mcbond_other1.038
r_scbond_it1.035
r_scbond_other1.035
r_angle_other_deg0.885
r_chiral_restr0.071
r_bond_refined_d0.008
r_gen_planes_refined0.004
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 Atoms2868
Nucleic Acid Atoms
Solvent Atoms145
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing