5A1G | pdb_00005a1g

The structure of Human MAT2A in complex with S-adenosylethionine and PPNP.

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2P02	PDB ENTRY 2P02

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		0.1 M IMIDAZOLE PH 7.0, 50 % MPD

Crystal Properties
Matthews coefficient	Solvent content
2	39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.39	α = 90
b = 94.39	β = 90
c = 117.39	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M	MIRRORS	2014-08-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1		Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.83	29.34	99.3	0.1	21.5	13.3		32401

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.83	1.9	97.5		0.81	3.4	12.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (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 Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2P02	1.83	58.69	32055	1633	99.37	0.12248	0.11982	0.14	0.1749	0.18	RANDOM	20.783

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]
3.06			-0.38		-2.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.702
r_sphericity_free	35.87
r_dihedral_angle_4_deg	20.264
r_dihedral_angle_3_deg	12.279
r_sphericity_bonded	9.726
r_dihedral_angle_1_deg	6.268
r_long_range_B_refined	3.773
r_long_range_B_other	3.772
r_scangle_other	2.664
r_scbond_it	2.178
r_scbond_other	2.178
r_mcangle_it	1.966
r_mcangle_other	1.966
r_mcbond_it	1.592
r_mcbond_other	1.591
r_angle_refined_deg	1.376
r_rigid_bond_restr	1.15
r_angle_other_deg	0.913
r_chiral_restr	0.081
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2954
Nucleic Acid Atoms
Solvent Atoms	278
Heterogen Atoms	65

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing