9LXQ | pdb_00009lxq

Crystal structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 100K

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	VAPOR DIFFUSION, HANGING DROP	5.4	293.2	15%(v/v)PEG#200, 0.1 M phosphate citrate pH 5.4, 5 mM MTA

Crystal Properties
Matthews coefficient	Solvent content
2.18040133	43.6234131

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.766	α = 90
b = 77.766	β = 90
c = 230.335	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	100	PIXEL	DECTRIS EIGER X 16M		2024-10-30	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	1.37	43.77	100	0.095	0.106	0.046	0.998	13.7	10		56744

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)
	1.37	1.4	99.9		0.823	0.928	0.419	0.672	2.7	9.1

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	1.37	43.77	56742	2771	99.923	0.122	0.1208	0.1208	0.1472	0.1472	16.764

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]
0.162	0.081		0.162		-0.524

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.148
r_dihedral_angle_2_deg	13.505
r_lrange_it	13.442
r_lrange_other	13.407
r_dihedral_angle_3_deg	12.418
r_scangle_it	10.66
r_scangle_other	10.657
r_scbond_it	7.685
r_scbond_other	7.682
r_dihedral_angle_1_deg	7.006
r_mcangle_it	6.592
r_mcangle_other	6.59
r_mcbond_it	4.551
r_mcbond_other	4.545
r_rigid_bond_restr	4.345
r_angle_refined_deg	2.007
r_angle_other_deg	0.67
r_nbd_other	0.26
r_symmetry_nbd_refined	0.223
r_nbd_refined	0.222
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.108
r_chiral_restr	0.105
r_symmetry_nbtor_other	0.089
r_symmetry_xyhbond_nbd_refined	0.087
r_dihedral_angle_other_2_deg	0.047
r_gen_planes_refined	0.012
r_bond_refined_d	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	96
Heterogen Atoms	56

Software

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