9JRZ | pdb_00009jrz

Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 323K

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
2.27757502	46.0287437

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.927	α = 90
b = 78.927	β = 90
c = 233.574	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	323	PIXEL	DECTRIS EIGER X 16M		2024-06-24	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	1.69	44.4	100	0.088	0.098	0.043	0.999	18.9	10.1		31854

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	1.69	1.72	100		1.347	1.503	0.662	0.68	1.9	9.9

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	1.69	39.495	31849	1628	99.965	0.112	0.1097	0.1098	0.1439	0.1439	27.792

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]
0.059	0.03		0.059		-0.192

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	19.528
r_lrange_other	19.524
r_scangle_it	16.738
r_scangle_other	16.733
r_dihedral_angle_6_deg	15.198
r_dihedral_angle_3_deg	13.633
r_scbond_it	11.46
r_scbond_other	11.46
r_mcangle_it	10.318
r_mcangle_other	10.316
r_dihedral_angle_2_deg	9.053
r_mcbond_it	7.111
r_mcbond_other	7.108
r_dihedral_angle_1_deg	6.85
r_rigid_bond_restr	4.461
r_angle_refined_deg	1.824
r_angle_other_deg	0.621
r_nbd_refined	0.217
r_nbd_other	0.213
r_symmetry_nbd_other	0.197
r_nbtor_refined	0.179
r_symmetry_nbd_refined	0.179
r_xyhbond_nbd_refined	0.127
r_symmetry_xyhbond_nbd_refined	0.12
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.084
r_dihedral_angle_other_2_deg	0.031
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
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	59
Heterogen Atoms	32

Software

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