9U5H | pdb_00009u5h

Crystal structure of MTAP from Aeropyrum pernix complex with MTA at 333K, 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, 0.1M phosphate citrate pH5.4, 5mM MTA. Crystals soaked in 0.1M potassium phosphate pH7.0 with 5mM MTA.

Crystal Properties
Matthews coefficient	Solvent content
2.27689242	46.0125628

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.875	α = 90
b = 78.875	β = 90
c = 233.812	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	333	PIXEL	DECTRIS EIGER X 16M		2024-12-21	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	1.67	44.41	100	0.059	0.066	0.029	1	25.2	10		32977

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)
	1.67	1.7	100		1.008	1.123	0.493	0.691	2.4	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	1.67	44.41	32975	1606	99.97	0.138	0.1368	0.1488	0.1644	0.1705	29.617

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]
0.268	0.134		0.268		-0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.55
r_dihedral_angle_3_deg	13.861
r_lrange_other	10.001
r_lrange_it	9.997
r_scangle_it	8.364
r_scangle_other	8.362
r_dihedral_angle_2_deg	8.137
r_dihedral_angle_1_deg	6.91
r_scbond_it	5.321
r_scbond_other	5.321
r_mcangle_it	4.071
r_mcangle_other	4.07
r_mcbond_it	2.893
r_mcbond_other	2.889
r_angle_refined_deg	1.946
r_angle_other_deg	0.643
r_nbd_refined	0.219
r_symmetry_nbd_other	0.2
r_nbd_other	0.185
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.122
r_symmetry_xyhbond_nbd_refined	0.116
r_symmetry_nbd_refined	0.097
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.086
r_dihedral_angle_other_2_deg	0.022
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
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