4YIH | pdb_00004yih

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4L57	PDB ENTRY 4L57

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	293	40 mM potassium phosphate monobasic, 6% PEG8000, 20% gycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.818	α = 111.18
b = 46.451	β = 88.16
c = 61.738	γ = 104.7

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	CCD	MARMOSAIC 225 mm CCD		2012-07-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.918	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	1.82	57.443	95.8	0.046	12.27	2.11		33500		-3	34.274

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	1.82	1.93	94.1		0.462	2.09

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	PDB ENTRY 4L57	1.82	57.44	33458	1672	96.11	0.1868	0.1847	0.19	0.2278	0.23	RANDOM	36.8837

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]
-0.82	-0.58	-0.2	0.69	0.87	-0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.563
r_dihedral_angle_4_deg	19.675
r_dihedral_angle_3_deg	13.029
r_dihedral_angle_1_deg	6.248
r_mcangle_it	2.693
r_angle_refined_deg	2.083
r_mcbond_it	1.987
r_mcbond_other	1.985
r_angle_other_deg	1.256
r_chiral_restr	0.171

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.563
r_dihedral_angle_4_deg	19.675
r_dihedral_angle_3_deg	13.029
r_dihedral_angle_1_deg	6.248
r_mcangle_it	2.693
r_angle_refined_deg	2.083
r_mcbond_it	1.987
r_mcbond_other	1.985
r_angle_other_deg	1.256
r_chiral_restr	0.171
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d	0.006
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3066
Nucleic Acid Atoms
Solvent Atoms	190
Heterogen Atoms	84

Software

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