9MAD | pdb_00009mad

Crystal structure of MTAP from Aeropyrum pernix complex with MTA at 323K, 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
2.27398872	45.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.851	α = 90
b = 78.851	β = 90
c = 233.656	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	323	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	1.59	44.39	100	0.053	0.059	0.026	1	28.3	10		38079

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)
	1.59	1.62	100		1.024	1.14	0.498	0.674	2.4	10.2

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	1.59	44.39	38078	1923	99.963	0.138	0.1372	0.1506	0.1619	0.1702	28.357

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]
0.239	0.12		0.239		-0.776

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.854
r_dihedral_angle_3_deg	13.711
r_lrange_other	10.482
r_lrange_it	10.481
r_scangle_it	8.488
r_scangle_other	8.485
r_dihedral_angle_2_deg	7.014
r_dihedral_angle_1_deg	6.983
r_scbond_it	5.464
r_scbond_other	5.464
r_mcangle_it	3.779
r_mcangle_other	3.778
r_mcbond_it	2.605
r_mcbond_other	2.604
r_angle_refined_deg	1.96
r_angle_other_deg	0.646
r_nbd_refined	0.223
r_symmetry_nbd_other	0.203
r_nbd_other	0.193
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.114
r_symmetry_nbd_refined	0.113
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.088
r_symmetry_xyhbond_nbd_refined	0.083
r_dihedral_angle_other_2_deg	0.066
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	56
Heterogen Atoms	25

Software

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