3F13

Crystal structure of putative nudix hydrolase family member from Chromobacterium violaceum

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	294	19% PEG 3350, 600mM ammonium chloride, pH 7.0, Vapor diffusion, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.95	α = 73.47
b = 43.877	β = 74.06
c = 55.967	γ = 62.66

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	MAR CCD 165 mm		2008-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID		APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.7	52.882	97.2	0.081	0.081	8.4	3.9	35983	34975			25.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.7	1.79	95.8		0.511	0.511	2	3.9	5017

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	SAD	THROUGHOUT	1.7	20	35950	34958	1752	97.24	0.223	0.221	0.264	RANDOM	35.158

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]
0.09	-0.93	1.35	1.21	-0.49	-0.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.087
r_dihedral_angle_4_deg	20.209
r_dihedral_angle_3_deg	17.319
r_dihedral_angle_1_deg	6.081
r_scangle_it	4.717
r_scbond_it	2.86
r_mcangle_it	1.685
r_angle_refined_deg	1.59
r_mcbond_it	0.948
r_chiral_restr	0.101

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.087
r_dihedral_angle_4_deg	20.209
r_dihedral_angle_3_deg	17.319
r_dihedral_angle_1_deg	6.081
r_scangle_it	4.717
r_scbond_it	2.86
r_mcangle_it	1.685
r_angle_refined_deg	1.59
r_mcbond_it	0.948
r_chiral_restr	0.101
r_bond_refined_d	0.015
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2244
Nucleic Acid Atoms
Solvent Atoms	188
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

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.