4NFL | pdb_00004nfl

Crystal structure of human mitochondrial 5'(3')-deoxyribonucleotidase in complex with the inhibitor NPB-T

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4L6A	PDB ENTRY 4L6A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	293	20 mM potassium phosphate monobasic, 8% PEG8000, 10% glycerol, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.65	α = 90
b = 73.65	β = 90
c = 105.91	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	CCD	RAYONIX MX-225		2012-01-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.97826	BESSY	14.2

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	1.375	52.078	90.9	0.041	26.11			56940		-3	23.35

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	1.375	1.45	61.9		0.674	1.91

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	PDB ENTRY 4L6A	1.375	46.73	56839	2886	92.95	0.1538	0.1526	0.15	0.176	0.18	RANDOM	22.2308

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]
-0.11			-0.11		0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.933
r_dihedral_angle_4_deg	12.02
r_dihedral_angle_3_deg	11.733
r_dihedral_angle_1_deg	6.006
r_mcangle_it	2.602
r_angle_refined_deg	2.044
r_mcbond_it	1.627
r_mcbond_other	1.626
r_angle_other_deg	0.955
r_chiral_restr	0.106

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.933
r_dihedral_angle_4_deg	12.02
r_dihedral_angle_3_deg	11.733
r_dihedral_angle_1_deg	6.006
r_mcangle_it	2.602
r_angle_refined_deg	2.044
r_mcbond_it	1.627
r_mcbond_other	1.626
r_angle_other_deg	0.955
r_chiral_restr	0.106
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1633
Nucleic Acid Atoms
Solvent Atoms	292
Heterogen Atoms	123

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling

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.