4TNY

Structural basis of cellular dNTP regulation, SAMHD1-dGTP-dATP-dGTP complex

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4BZB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		298	SPG buffer, PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.253	α = 90
b = 141.874	β = 116.38
c = 98.333	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	PSI PILATUS 6M		2013-09-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.1	NSLS	X25

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.6	50	99.6	0.153	5.9	3.8		66014

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.64	92.8			3	3038

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	4BZB	2.6	50	65672	3322	98.65	0.2152	0.2136	0.2439	RANDOM	41.654

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]
1.53		-0.65	0.06		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.024
r_dihedral_angle_3_deg	15.827
r_dihedral_angle_4_deg	13.622
r_dihedral_angle_1_deg	5.199
r_mcangle_it	3.694
r_mcbond_it	2.327
r_mcbond_other	2.327
r_angle_refined_deg	1.49
r_angle_other_deg	0.9
r_chiral_restr	0.093

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.024
r_dihedral_angle_3_deg	15.827
r_dihedral_angle_4_deg	13.622
r_dihedral_angle_1_deg	5.199
r_mcangle_it	3.694
r_mcbond_it	2.327
r_mcbond_other	2.327
r_angle_refined_deg	1.49
r_angle_other_deg	0.9
r_chiral_restr	0.093
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15732
Nucleic Acid Atoms
Solvent Atoms	15
Heterogen Atoms	372

Software

Software
Software Name	Purpose
HKL-2000	data reduction
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.