2GM3 | pdb_00002gm3

Crystal Structure of an Universal Stress Protein Family Protein from Arabidopsis Thaliana At3g01520 with AMP Bound

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, 0.005 MES PH 7.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (18% PEG 2K, 5% DMSO, 0.10 M PIPES PH 6.5) Crystals cryo-protected with 20% PEG 2K, 0.1 M TRIS PH 8, and a final concentration of 20 % Ethylene glycol, temperature 293K, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.24	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.351	α = 75.45
b = 65.662	β = 75.04
c = 73.014	γ = 66.11

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 300 mm CCD	HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR	2005-06-13	M	SINGLE WAVELENGTH
2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.97934	APS	22-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	2.5	40.7	97.2	0.058	9.913	3.7		36006

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	2.5	2.59	89.4		0.239	4.406	3	3309

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 (All)	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	SAD	THROUGHOUT	2.461	40.7	36006	1800	96.822	0.221	0.22065	0.2185	0.2247	0.2607	0.2598	Random	60.244

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]
-0.171	-0.933	1.28	0.245	-0.48	0.262

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.463
r_dihedral_angle_4_deg	21.711
r_dihedral_angle_3_deg	17.647
r_dihedral_angle_1_deg	5.675
r_scangle_it	2.18
r_angle_refined_deg	1.501
r_scbond_it	1.445
r_mcangle_it	0.942
r_mcbond_it	0.573
r_chiral_restr	0.374

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.463
r_dihedral_angle_4_deg	21.711
r_dihedral_angle_3_deg	17.647
r_dihedral_angle_1_deg	5.675
r_scangle_it	2.18
r_angle_refined_deg	1.501
r_scbond_it	1.445
r_mcangle_it	0.942
r_mcbond_it	0.573
r_chiral_restr	0.374
r_nbtor_refined	0.31
r_symmetry_hbond_refined	0.262
r_nbd_refined	0.222
r_symmetry_vdw_refined	0.196
r_xyhbond_nbd_refined	0.16
r_bond_refined_d	0.016
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7084
Nucleic Acid Atoms
Solvent Atoms	13
Heterogen Atoms	138

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
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 R01GM157729.