9JD2 | pdb_00009jd2

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

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

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.172

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	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	1.62	39.52	100	0.141	0.157	0.069	0.999	9.8	9.9		36182

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)
	1.62	1.65	100		2.545	2.838	1.246	0.344	1.1	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	1.62	38.944	36182	1820	99.953	0.125	0.1228	0.1217	0.1676	0.1662	28.651

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]
-0.31	-0.155		-0.31		1.005

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	20.207
r_lrange_other	20.203
r_scangle_it	16.317
r_scangle_other	16.312
r_dihedral_angle_6_deg	15.216
r_dihedral_angle_3_deg	12.925
r_scbond_it	10.958
r_scbond_other	10.957
r_mcangle_it	10.841
r_mcangle_other	10.838
r_dihedral_angle_2_deg	8.261
r_mcbond_it	7.218
r_mcbond_other	7.217
r_dihedral_angle_1_deg	6.903
r_rigid_bond_restr	4.187
r_angle_refined_deg	1.688
r_angle_other_deg	0.591
r_symmetry_nbd_refined	0.233
r_nbd_other	0.218
r_nbd_refined	0.217
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.175
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.087
r_symmetry_nbtor_other	0.083
r_dihedral_angle_other_2_deg	0.018
r_bond_refined_d	0.009
r_gen_planes_refined	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	47
Heterogen Atoms	25

Software

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