9U76 | pdb_00009u76

Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 353K 1.77 angstrom

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.

Crystal Properties
Matthews coefficient	Solvent content
2.28364396	46.1721764

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.048	α = 90
b = 79.048	β = 90
c = 233.48	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	353	PIXEL	DECTRIS EIGER X 16M		2024-06-02	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	1.77	39.52	100	0.112	0.124	0.054	0.999	12.7	9.9		27838

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)
	1.77	1.81	100		1.253	1.416	0.652	0.691	2.5	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	1.77	38.944	27837	1399	99.939	0.142	0.1406	0.1535	0.1754	0.1801	30.513

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]
0.3	0.15		0.3		-0.972

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.255
r_dihedral_angle_3_deg	13.609
r_lrange_other	10.885
r_lrange_it	10.884
r_dihedral_angle_2_deg	8.641
r_scangle_it	8.544
r_scangle_other	8.542
r_dihedral_angle_1_deg	7.054
r_scbond_it	5.334
r_scbond_other	5.334
r_mcangle_it	4.363
r_mcangle_other	4.362
r_mcbond_it	2.977
r_mcbond_other	2.977
r_angle_refined_deg	1.835
r_angle_other_deg	0.623
r_nbd_refined	0.213
r_nbd_other	0.206
r_symmetry_nbd_refined	0.201
r_symmetry_nbd_other	0.198
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.129
r_symmetry_xyhbond_nbd_refined	0.105
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.085
r_dihedral_angle_other_2_deg	0.019
r_gen_planes_refined	0.011
r_bond_refined_d	0.009
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	45
Heterogen Atoms	25

Software

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