6YOM | pdb_00006yom

Crystal structure of tetrameric human D137N-SAMHD1 (residues 109-626) with XTP, dATP, dCMPNPP, Mn and Mg

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6TX0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	0.1 M Bistris methane-HCl pH 6, 15% (w/v) PEG 3350, 0.05 M MgCl2

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.298	α = 90
b = 105.298	β = 90
c = 195.629	γ = 90

Symmetry
Space Group	P 43 21 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 PILATUS 6M		2018-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	1.9075	Diamond	I03

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	3.25	195.63	100	0.204	0.211	0.053	0.997	10.5	15.4		18094			86.2

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	3.25	3.31	99.44		1.336	1.381	0.349	0.752	2.1	15.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6TX0	3.25	92.72	17100	931	99.92	0.1789	0.1759	0.18	0.2359	0.24	RANDOM	76.14

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]
-0.13			-0.13		0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.855
r_dihedral_angle_3_deg	15.548
r_dihedral_angle_4_deg	15.507
r_dihedral_angle_1_deg	6.856
r_angle_refined_deg	1.846
r_angle_other_deg	1.083
r_chiral_restr	0.097
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.855
r_dihedral_angle_3_deg	15.548
r_dihedral_angle_4_deg	15.507
r_dihedral_angle_1_deg	6.856
r_angle_refined_deg	1.846
r_angle_other_deg	1.083
r_chiral_restr	0.097
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7210
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	188

Software

Software
Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction

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.