6G2M | pdb_00006g2m

Crystal structure of human mitochondrial 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	4YIK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	291	100mM CHES, pH 9.5, 20% PEG8000

Crystal Properties
Matthews coefficient	Solvent content
3.11	60.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.858	α = 90
b = 73.858	β = 90
c = 106.121	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		2015-09-29	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	1.37	46.86	99.9	0.061	1	23.56	10.1		62295			22.8

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	1.37	1.45	99.7		1.248	0.683	1.93	10.2

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	FOURIER SYNTHESIS	THROUGHOUT	4YIK	1.37	46.86	60197	2100	99.91	0.1258	0.1249	0.13	0.1505	0.15	RANDOM	20.552

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]
-0.39			-0.39		0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.252
r_sphericity_free	20.301
r_dihedral_angle_4_deg	14.986
r_rigid_bond_restr	11.219
r_dihedral_angle_3_deg	11.093
r_sphericity_bonded	7.614
r_dihedral_angle_1_deg	5.873
r_angle_other_deg	2.263
r_angle_refined_deg	2.117
r_chiral_restr	0.198

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.252
r_sphericity_free	20.301
r_dihedral_angle_4_deg	14.986
r_rigid_bond_restr	11.219
r_dihedral_angle_3_deg	11.093
r_sphericity_bonded	7.614
r_dihedral_angle_1_deg	5.873
r_angle_other_deg	2.263
r_angle_refined_deg	2.117
r_chiral_restr	0.198
r_bond_refined_d	0.017
r_gen_planes_refined	0.012
r_gen_planes_other	0.007
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1608
Nucleic Acid Atoms
Solvent Atoms	290
Heterogen Atoms	62

Software

Software
Software Name	Purpose
XDS	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 R01GM157729.