9VS8 | pdb_00009vs8

Intermediate state structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix at high temperature (363K) after 10 minutes reaction with substrate

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, methylcellulose 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
2.28471565	46.1974258

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.042	α = 90
b = 79.042	β = 90
c = 233.625	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	363	PIXEL	DECTRIS EIGER X 16M		2025-07-02	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	2.08	44.43	100	0.194	0.215	0.092	0.997	13.2	10.2		17322

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)
	2.08	2.14	100		1.123	1.242	0.526	0.674	2.6	10.7

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	2.08	44.43	17322	894	99.954	0.145	0.1439	0.156	0.1741	0.182	32.015

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]
0.285	0.143		0.285		-0.926

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.854
r_dihedral_angle_6_deg	14.683
r_lrange_it	10.455
r_lrange_other	10.454
r_dihedral_angle_2_deg	8.18
r_scangle_it	8.084
r_scangle_other	8.081
r_dihedral_angle_1_deg	7.416
r_scbond_it	4.967
r_scbond_other	4.966
r_mcangle_it	4.386
r_mcangle_other	4.384
r_mcbond_it	2.824
r_mcbond_other	2.821
r_angle_refined_deg	1.746
r_angle_other_deg	0.564
r_nbd_refined	0.213
r_symmetry_nbd_other	0.196
r_nbd_other	0.187
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.129
r_symmetry_xyhbond_nbd_refined	0.118
r_symmetry_nbd_refined	0.092
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.081
r_dihedral_angle_other_2_deg	0.055
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
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	30
Heterogen Atoms	25

Software

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