9MA4 | pdb_00009ma4

Crystal structure of MTAP from Aeropyrum pernix complex with MTA at 343K, Soaked in potassium phosphate pH7.0 with MTA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WTA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	COUNTER-DIFFUSION	5.4	293.2	The mixture of protein solution and agarose was filled into a glass capillary, and the capillary was immersed in the reservoir solution for crystallization. The composition of the reservoir solution was as follows.15%(v/v)PEG#200,0.1 M phosphate citrate pH 5.4, 5 mM MTA. Crystals soaked in 0.1M potassium phosphate pH7.0 with 5mM MTA.

Crystal Properties
Matthews coefficient	Solvent content
2.28745079	46.2617569

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.021	α = 90
b = 79.021	β = 90
c = 234.029	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	343	PIXEL	DECTRIS EIGER X 16M		2025-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.98	Photon Factory	BL-17A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.72	44.47	100	0.098	0.108	0.047	1	23.7	10		30381

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.72	1.75	100		1.2	1.343	0.596	0.675	2.3	9.7

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1WTA	1.72	44.47	30379	1473	99.961	0.139	0.1373	0.1494	0.1683	0.1782	29.637

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]
0.293	0.147		0.293		-0.952

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.452
r_dihedral_angle_3_deg	14.512
r_dihedral_angle_2_deg	10.699
r_lrange_it	10.514
r_lrange_other	10.514
r_scangle_it	8.408
r_scangle_other	8.406
r_dihedral_angle_1_deg	7.301
r_scbond_it	5.303
r_scbond_other	5.303
r_mcangle_it	4.183
r_mcangle_other	4.181
r_mcbond_it	2.852
r_mcbond_other	2.85
r_angle_refined_deg	1.926
r_angle_other_deg	0.628
r_nbd_refined	0.216
r_symmetry_nbd_other	0.196
r_nbd_other	0.189
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.146
r_symmetry_xyhbond_nbd_refined	0.102
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.088
r_symmetry_nbd_refined	0.068
r_dihedral_angle_other_2_deg	0.039
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2142
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms	25

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
MOLREP	phasing
Aimless	data scaling
XDS	data reduction