3BWV

Crystal structure of deoxyribonucleotidase-like protein (NP_764060.1) from Staphylococcus epidermidis ATCC 12228 at 1.55 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	NANODROP, 17.6% PEG 3350, 0.4M Magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.87	34.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.31	α = 71.93
b = 40.27	β = 75.08
c = 55.31	γ = 83.62

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 325 mm CCD	Flat mirror (vertical focusing)	2007-12-09	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97908, 0.97959	SSRL	BL11-1

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	1.54	29.235	92.8	0.067	4.92			43195		-3	27.438

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	1.54	1.6	75.2		0.529	1.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.55	29.235	43194	2176	94.9	0.184	0.182	0.223	RANDOM	19.268

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]
0.12	-0.21	-0.58	-0.79	0.77	0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.647
r_dihedral_angle_4_deg	21.593
r_dihedral_angle_3_deg	13.772
r_dihedral_angle_1_deg	5.971
r_scangle_it	4.812
r_scbond_it	3.105
r_mcangle_it	1.748
r_angle_refined_deg	1.634
r_angle_other_deg	1.044
r_mcbond_it	1.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.647
r_dihedral_angle_4_deg	21.593
r_dihedral_angle_3_deg	13.772
r_dihedral_angle_1_deg	5.971
r_scangle_it	4.812
r_scbond_it	3.105
r_mcangle_it	1.748
r_angle_refined_deg	1.634
r_angle_other_deg	1.044
r_mcbond_it	1.004
r_mcbond_other	0.301
r_chiral_restr	0.104
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2700
Nucleic Acid Atoms
Solvent Atoms	181
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	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 R01GM133198.