8WS2 | pdb_00008ws2

Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine

X-RAY DIFFRACTION

---

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#200,0.1 M phosphate citrate pH 5.4, 5 mM MTA

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.646	α = 90
b = 77.646	β = 90
c = 230.39	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		2024-06-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	1.0	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	1.22	43.74	100	0.107	0.12	0.053	0.999	13.2	10		79813

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	1.22	1.24			2.221	2.48	1.092	0.382		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	1.22	38.853	79810	4025	99.98	0.143	0.1422	0.1424	0.166	0.1644	15.772

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]
0.006	0.003		0.006		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.06
r_dihedral_angle_3_deg	12.682
r_lrange_it	11.891
r_lrange_other	11.89
r_dihedral_angle_2_deg	10.009
r_scangle_it	8.795
r_scangle_other	8.792
r_dihedral_angle_1_deg	6.92
r_scbond_other	6.353
r_scbond_it	6.352
r_mcangle_it	5.739
r_mcangle_other	5.737
r_mcbond_it	3.987
r_mcbond_other	3.983
r_rigid_bond_restr	3.908
r_angle_refined_deg	1.93
r_angle_other_deg	0.665
r_nbd_refined	0.224
r_nbd_other	0.209
r_symmetry_nbd_other	0.205
r_nbtor_refined	0.18
r_symmetry_nbd_refined	0.162
r_dihedral_angle_other_2_deg	0.153
r_symmetry_xyhbond_nbd_refined	0.136
r_xyhbond_nbd_refined	0.119
r_chiral_restr	0.101
r_symmetry_nbtor_other	0.084
r_xyhbond_nbd_other	0.064
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	150
Heterogen Atoms	49

Software

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