9LYE | pdb_00009lye

Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix 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	15%(v/v)PEG#200, 0.1 M phosphate citrate pH 5.4

Crystal Properties
Matthews coefficient	Solvent content
2.19770145	44.0672035

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.953	α = 90
b = 77.953	β = 90
c = 231.05	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	43.89	100	0.109	0.122	0.053	0.998	12.8	10.1		57204

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	1.39	100		0.873	0.987	0.454	0.677	2.6	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	1.37	43.89	57203	2787	99.976	0.121	0.1192	0.1194	0.1461	0.1457	14.744

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]
0.046	0.023		0.046		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.763
r_dihedral_angle_2_deg	12.853
r_lrange_it	12.273
r_lrange_other	12.152
r_dihedral_angle_3_deg	11.469
r_scangle_it	10.112
r_scangle_other	10.109
r_scbond_it	7.556
r_scbond_other	7.555
r_dihedral_angle_1_deg	6.778
r_mcangle_it	5.159
r_mcangle_other	5.158
r_rigid_bond_restr	4.382
r_mcbond_it	3.574
r_mcbond_other	3.567
r_angle_refined_deg	1.846
r_angle_other_deg	0.644
r_nbd_refined	0.221
r_symmetry_nbd_other	0.212
r_nbd_other	0.203
r_dihedral_angle_other_2_deg	0.188
r_symmetry_xyhbond_nbd_refined	0.181
r_nbtor_refined	0.18
r_symmetry_nbd_refined	0.177
r_xyhbond_nbd_refined	0.111
r_chiral_restr	0.103
r_symmetry_nbtor_other	0.086
r_bond_refined_d	0.012
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	112
Heterogen Atoms	108

Software

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