9JKU | pdb_00009jku

Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 333K

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
2.27440357	45.9534874

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.924	α = 90
b = 78.924	β = 90
c = 233.512	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	333	PIXEL	DECTRIS PILATUS3 S 6M		2024-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	0.98	Photon Factory	BL-5A

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	1.61	44.39	100	0.071	0.079	0.034	0.999	23.7	10		36745

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.61	1.64	100		1.029	0.496	0.672	2.6	10.1

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	1.61	44.39	36744	1847	99.967	0.141	0.1398	0.1513	0.1683	0.1742	27.114

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]
0.14	0.07		0.14		-0.453

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.136
r_dihedral_angle_3_deg	13.686
r_lrange_it	9.911
r_lrange_other	9.911
r_dihedral_angle_2_deg	9.445
r_scangle_it	8.045
r_scangle_other	8.043
r_dihedral_angle_1_deg	6.846
r_scbond_it	5.125
r_scbond_other	5.125
r_mcangle_it	4.528
r_mcangle_other	4.527
r_mcbond_it	3.026
r_mcbond_other	3.025
r_angle_refined_deg	1.993
r_angle_other_deg	0.66
r_nbd_refined	0.221
r_symmetry_nbd_other	0.201
r_nbd_other	0.188
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.128
r_chiral_restr	0.1
r_symmetry_nbd_refined	0.1
r_symmetry_nbtor_other	0.088
r_symmetry_xyhbond_nbd_refined	0.069
r_dihedral_angle_other_2_deg	0.047
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	54
Heterogen Atoms	25

Software

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