9M5W | pdb_00009m5w

Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 343K 1.58 angstrom

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 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 pH 5.4, 5mM MTA

Crystal Properties
Matthews coefficient	Solvent content
2.27741838	46.025032

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.94	α = 90
b = 78.94	β = 90
c = 233.481	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	343	PIXEL	DECTRIS EIGER X 16M		2024-11-24	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	1.58	44.39	99.9	0.058	0.065	0.028	1	25.7	10		38817

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)
	1.58	1.61	100		1.047	1.166	0.509	0.669	2.4	10.2

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	1.58	44.39	38816	1944	99.912	0.142	0.1412	0.1534	0.1628	0.1696	27.383

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]
0.205	0.103		0.205		-0.666

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.893
r_dihedral_angle_3_deg	13.456
r_dihedral_angle_2_deg	9.857
r_lrange_other	9.835
r_lrange_it	9.83
r_scangle_it	7.996
r_scangle_other	7.994
r_dihedral_angle_1_deg	6.999
r_scbond_it	5.21
r_scbond_other	5.208
r_mcangle_it	3.785
r_mcangle_other	3.784
r_mcbond_it	2.602
r_mcbond_other	2.602
r_angle_refined_deg	1.981
r_angle_other_deg	0.651
r_symmetry_nbd_refined	0.242
r_nbd_refined	0.218
r_nbd_other	0.201
r_symmetry_nbd_other	0.2
r_nbtor_refined	0.181
r_symmetry_xyhbond_nbd_refined	0.141
r_xyhbond_nbd_refined	0.121
r_chiral_restr	0.101
r_symmetry_nbtor_other	0.087
r_xyhbond_nbd_other	0.054
r_bond_refined_d	0.012
r_gen_planes_refined	0.012
r_dihedral_angle_other_2_deg	0.006
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	48
Heterogen Atoms	32

Software

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