6G2N

Crystal structure of human cytosolic 5'(3')-deoxyribonucleotidase in complex with the inhibitor PB-PAU

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	291	Morpheus H2, 0.1M MES/imidazole pH 6.5, 10% PEG 8000, 20% ethylene glycol, 0.02M of each amino acid,

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.877	α = 67.86
b = 47.231	β = 88.69
c = 61.795	γ = 77.37

Symmetry
Space Group	P 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	DECTRIS PILATUS 6M		2016-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	1.4	42.41	87.8	0.026	1	18.84	2.22		68116			27.42

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.49	87.9		0.556	0.7414		2.21

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	4YIH	1.4	42.41	66015	2100	87.97	0.1521	0.1508	0.192	RANDOM	27.295

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]
-0.41	-1.14	0.09	1.7	0.22	-1.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.574
r_dihedral_angle_4_deg	19.961
r_sphericity_free	16.034
r_dihedral_angle_3_deg	13.109
r_sphericity_bonded	8.003
r_rigid_bond_restr	6.105
r_dihedral_angle_1_deg	5.95
r_angle_refined_deg	2.02
r_angle_other_deg	1.966
r_chiral_restr	0.185

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.574
r_dihedral_angle_4_deg	19.961
r_sphericity_free	16.034
r_dihedral_angle_3_deg	13.109
r_sphericity_bonded	8.003
r_rigid_bond_restr	6.105
r_dihedral_angle_1_deg	5.95
r_angle_refined_deg	2.02
r_angle_other_deg	1.966
r_chiral_restr	0.185
r_bond_refined_d	0.017
r_gen_planes_refined	0.01
r_gen_planes_other	0.008
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3129
Nucleic Acid Atoms
Solvent Atoms	294
Heterogen Atoms	70

Software

Software
Software Name	Purpose
XDS	data reduction
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 R01GM157729.