5TC5

Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with butylthio-DADMe-Immucillin-A and chloride

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1K27

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	295	Protein (15 mg/mL); Reservoir (3 M sodium chloride and 0.1 M sodium acetate (pH 4.5))

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.522	α = 90
b = 121.927	β = 90
c = 192.522	γ = 90

Symmetry
Space Group	I 2 2 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	CCD	RAYONIX MX225HE		2015-02-13	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)	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	1.96	50	99.7	0.074	0.08	16.86	7.48		75649		-3	39.471

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.96	2.08	99		0.782	2.77	7.48

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	1K27	1.96	25	71803	3779	99.76	0.191	0.1896	0.2166	RANDOM	51.803

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]
-2.52			1.54		0.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.766
r_dihedral_angle_4_deg	17.184
r_dihedral_angle_3_deg	13.663
r_dihedral_angle_1_deg	6.417
r_mcangle_it	3.466
r_mcbond_it	2.492
r_mcbond_other	2.491
r_angle_refined_deg	1.858
r_angle_other_deg	1.605
r_chiral_restr	0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.766
r_dihedral_angle_4_deg	17.184
r_dihedral_angle_3_deg	13.663
r_dihedral_angle_1_deg	6.417
r_mcangle_it	3.466
r_mcbond_it	2.492
r_mcbond_other	2.491
r_angle_refined_deg	1.858
r_angle_other_deg	1.605
r_chiral_restr	0.12
r_bond_refined_d	0.018
r_gen_planes_refined	0.011
r_bond_other_d	0.009
r_gen_planes_other	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6261
Nucleic Acid Atoms
Solvent Atoms	228
Heterogen Atoms	73

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing
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 R01GM157729.