9U79 | pdb_00009u79

Crystal structure of MTAP from Aeropyrum pernix complex with MTA at 100K, 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	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
2.17883253	43.58209

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.66	α = 90
b = 77.66	β = 90
c = 230.798	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	100	PIXEL	DECTRIS EIGER X 16M		2024-12-09	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	1.19	43.79	100	0.053	0.06	0.026	1	21.1	9.7		86141

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)
	1.19	1.21	100		0.597	0.666	0.294	0.665	3.1	9.9

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	1.19	43.79	86126	4322	99.967	0.131	0.1299	0.132	0.1572	0.1564	16.29

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]
0.143	0.071		0.143		-0.464

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.885
r_lrange_it	12.54
r_lrange_other	12.481
r_dihedral_angle_3_deg	12.162
r_dihedral_angle_2_deg	10.308
r_scangle_it	10.014
r_scangle_other	10.011
r_scbond_it	7.227
r_scbond_other	7.224
r_dihedral_angle_1_deg	6.91
r_mcangle_it	6.521
r_mcangle_other	6.519
r_mcbond_it	4.565
r_mcbond_other	4.56
r_rigid_bond_restr	4.289
r_angle_refined_deg	1.904
r_angle_other_deg	0.689
r_nbd_refined	0.219
r_symmetry_nbd_other	0.195
r_nbd_other	0.191
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.129
r_dihedral_angle_other_2_deg	0.123
r_symmetry_nbd_refined	0.115
r_chiral_restr	0.109
r_symmetry_nbtor_other	0.083
r_symmetry_xyhbond_nbd_refined	0.083
r_gen_planes_refined	0.013
r_bond_refined_d	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	133
Heterogen Atoms	59

Software

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