5EUB

Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with 2-amino-MTA and sulfate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	Protein 15 mg/mL, Reservoir 0.2 M magnesium chloride, 20% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.504	α = 90
b = 121.504	β = 90
c = 45.328	γ = 120

Symmetry
Space Group	P 3 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX225HE		2015-07-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97931	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.8	50	98.7	0.091	0.099	0.038	9.5	6		35008			25

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	1.8	1.83	99.8		0.738	0.809	0.325	0.874	2.27	5.9	1719

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1K27	1.81	25	33251	1701	98.47	0.1703	0.1691	0.1928	RANDOM	25.86

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]
-1.14	-0.57		-1.14		3.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.001
r_dihedral_angle_4_deg	13.47
r_dihedral_angle_3_deg	12.521
r_dihedral_angle_1_deg	6.1
r_mcangle_it	2.184
r_angle_refined_deg	1.456
r_mcbond_it	1.435
r_mcbond_other	1.433
r_angle_other_deg	0.922
r_chiral_restr	0.073

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.001
r_dihedral_angle_4_deg	13.47
r_dihedral_angle_3_deg	12.521
r_dihedral_angle_1_deg	6.1
r_mcangle_it	2.184
r_angle_refined_deg	1.456
r_mcbond_it	1.435
r_mcbond_other	1.433
r_angle_other_deg	0.922
r_chiral_restr	0.073
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2072
Nucleic Acid Atoms
Solvent Atoms	180
Heterogen Atoms	44

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.