8P1W | pdb_00008p1w

Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with allosteric compound STL232591

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5A1I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	0.10 M HEPES pH 8.0, 8 - 12%(v/v) Ethylene glycol, 8 - 10.0% (w/v) PEG8000

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.132	α = 90
b = 93.785	β = 90
c = 116.706	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 EIGER X 16M		2022-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9999	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rpim I (All)	CC (Half)	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	1.15	58.91	99.4	0.057	0.053	0.02	0.999	14.8	7.1		132552

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.15	1.15			0.817	0.684	0.427	0.602	1.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (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 DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.15	58.909	132550	10245	99.422	0.113	0.1115	0.11	0.1292	0.13	15.494

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]
0.72			-0.316		-0.404

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.866
r_dihedral_angle_4_deg	18.997
r_dihedral_angle_3_deg	10.981
r_dihedral_angle_1_deg	6.864
r_dihedral_angle_other_3_deg	3.38
r_lrange_it	2.494
r_lrange_other	2.068
r_rigid_bond_restr	1.962
r_scangle_it	1.683
r_scangle_other	1.683
r_angle_other_deg	1.534
r_angle_refined_deg	1.468
r_dihedral_angle_other_6_deg	1.457
r_scbond_other	1.368
r_scbond_it	1.367
r_mcangle_it	1.191
r_mcangle_other	1.191
r_mcbond_it	0.88
r_mcbond_other	0.88
r_nbd_refined	0.208
r_symmetry_xyhbond_nbd_refined	0.193
r_nbd_other	0.188
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.15
r_symmetry_nbd_refined	0.116
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.076
r_bond_other_d	0.009
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2963
Nucleic Acid Atoms
Solvent Atoms	406
Heterogen Atoms	75

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
autoPROC	data scaling
PHASER	phasing