3WPP | pdb_00003wpp

Acinetobacter sp. Tol 5 AtaA YDD-DALL3 domains in C-terminal stalk fused to GCN4 adaptors (CstalkC1iii)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YO2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	0.67% PEG 2000 MME, 67mM HEPES, 667mM Succinic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.35	63.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.46	α = 90
b = 43.46	β = 90
c = 825.36	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS VII		2013-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.95	19.64	99.5			23200	23200

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.07	98.8		0.469	0.499	4.04

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2YO2	1.952	19.64	23198	23198	1160	99.57	0.1806	0.1806	0.1793	0.19	0.2053	0.21	RANDOM	35.524

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]
0.21	0.21		0.21		-0.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.77
r_sphericity_free	29.456
r_sphericity_bonded	18.99
r_dihedral_angle_3_deg	15.366
r_dihedral_angle_1_deg	5.352
r_mcangle_it	5.242
r_mcbond_it	4.338
r_mcbond_other	4.338
r_rigid_bond_restr	3.809
r_dihedral_angle_4_deg	2.423

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.77
r_sphericity_free	29.456
r_sphericity_bonded	18.99
r_dihedral_angle_3_deg	15.366
r_dihedral_angle_1_deg	5.352
r_mcangle_it	5.242
r_mcbond_it	4.338
r_mcbond_other	4.338
r_rigid_bond_restr	3.809
r_dihedral_angle_4_deg	2.423
r_angle_refined_deg	1.38
r_angle_other_deg	0.82
r_chiral_restr	0.081
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	786
Nucleic Acid Atoms
Solvent Atoms	110
Heterogen Atoms	1

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
XDS	data reduction
XDS	data scaling
MOLREP	phasing

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.