9U5I | pdb_00009u5i

Crystal structure of MTAP from Aeropyrum pernix complex with MTA at 293K, 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 intou 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, 0.1M phosphate citarate pH5.4, 5mM MTA. Crystals soaked in 0.1M potassium phosphate pH7.0 with 5mM MTA.

Crystal Properties
Matthews coefficient	Solvent content
2.26955032	45.8379135

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.788	α = 90
b = 78.788	β = 90
c = 233.573	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	293	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	1.64	44.36	100	0.069	0.077	0.033	1	25	10		34662

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)
	1.64	1.67	100		0.976	1.089	0.475	0.675	2.8	10

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	1.64	44.36	34660	1685	99.968	0.141	0.1397	0.152	0.1592	0.168	25.255

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]
0.195	0.098		0.195		-0.634

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.283
r_dihedral_angle_3_deg	13.669
r_lrange_it	8.826
r_lrange_other	8.823
r_dihedral_angle_2_deg	8.528
r_scangle_it	7.198
r_scangle_other	7.196
r_dihedral_angle_1_deg	7.001
r_scbond_it	4.641
r_scbond_other	4.64
r_mcangle_it	3.173
r_mcangle_other	3.172
r_mcbond_it	2.231
r_mcbond_other	2.231
r_angle_refined_deg	1.923
r_angle_other_deg	0.642
r_nbd_refined	0.214
r_symmetry_nbd_other	0.198
r_nbtor_refined	0.181
r_nbd_other	0.176
r_xyhbond_nbd_refined	0.13
r_chiral_restr	0.096
r_symmetry_xyhbond_nbd_refined	0.089
r_symmetry_nbtor_other	0.086
r_symmetry_nbd_refined	0.074
r_dihedral_angle_other_2_deg	0.044
r_gen_planes_refined	0.011
r_bond_refined_d	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	70
Heterogen Atoms	25

Software

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