9JSS | pdb_00009jss

Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 293K

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.10%(v/v)PEG#200,0.1 M phosphate citrate pH 5.4, 2.5 mM MTA

Crystal Properties
Matthews coefficient	Solvent content
2.27516794	45.9716454

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.876	α = 90
b = 78.876	β = 90
c = 233.629	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	293	PIXEL	DECTRIS EIGER X 16M		2024-02-10	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	1.39	44.39	100	0.056	0.062	0.027	0.999	19.9	10		56723

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	1.39	1.41	100		1.137	1.269	0.556	0.685	2.2	9.7

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	1.39	44.39	56722	2773	99.982	0.118	0.1169	0.1162	0.1431	0.142	23.32

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]
-0.092	-0.046		-0.092		0.299

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	19.609
r_lrange_other	19.605
r_dihedral_angle_6_deg	15.771
r_scangle_it	15.613
r_scangle_other	15.609
r_dihedral_angle_3_deg	12.204
r_mcangle_it	11.473
r_mcangle_other	11.469
r_scbond_it	10.936
r_scbond_other	10.935
r_dihedral_angle_2_deg	9.892
r_mcbond_it	8.293
r_mcbond_other	8.283
r_dihedral_angle_1_deg	7.142
r_rigid_bond_restr	4.837
r_angle_refined_deg	1.992
r_angle_other_deg	0.688
r_symmetry_nbd_refined	0.296
r_nbd_refined	0.242
r_nbd_other	0.235
r_symmetry_nbd_other	0.211
r_nbtor_refined	0.183
r_dihedral_angle_other_2_deg	0.157
r_symmetry_xyhbond_nbd_refined	0.146
r_xyhbond_nbd_refined	0.124
r_chiral_restr	0.105
r_symmetry_nbtor_other	0.087
r_bond_refined_d	0.012
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	2153
Nucleic Acid Atoms
Solvent Atoms	78
Heterogen Atoms	32

Software

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