2GMY

Crystal Structure of a Protein of Unknown Function ATU0492 from Agrobacterium tumefaciens, Putative Antioxidant Defence Protein AhpD

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	2M NH4Sulphate, 2% PEG400, 0.1M Hepes Na, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.009	α = 90
b = 75.009	β = 90
c = 148.755	γ = 120

Symmetry
Space Group	P 31

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	ADSC QUANTUM 315	mirrors	2005-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9798	APS	19-ID

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	1.6	65	99.73	0.084	15.74	3.5	117258	116941	2	2	20

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	1.6	1.642	98.88		0.55	1.44	2.7	8654

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.6	64.96	117258	116941	6180	99.73	0.16833	0.16833	0.16714	0.19089	RANDOM	19.766

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]
-0.44	-0.22		-0.44		0.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.061
r_dihedral_angle_4_deg	17.401
r_dihedral_angle_3_deg	12.318
r_dihedral_angle_1_deg	4.604
r_scangle_it	3.35
r_scbond_it	2.091
r_mcangle_it	1.142
r_angle_refined_deg	1.12
r_mcbond_it	0.716
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.061
r_dihedral_angle_4_deg	17.401
r_dihedral_angle_3_deg	12.318
r_dihedral_angle_1_deg	4.604
r_scangle_it	3.35
r_scbond_it	2.091
r_mcangle_it	1.142
r_angle_refined_deg	1.12
r_mcbond_it	0.716
r_nbtor_refined	0.305
r_nbd_refined	0.203
r_symmetry_vdw_refined	0.162
r_symmetry_hbond_refined	0.154
r_xyhbond_nbd_refined	0.124
r_chiral_restr	0.075
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6963
Nucleic Acid Atoms
Solvent Atoms	767
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
HKL-3000	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	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.