3QTB | pdb_00003qtb

Structure of the universal stress protein from Archaeoglobus fulgidus in complex with dAMP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DLO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	0.2M ammonium sulfate, 0.1M BIS-TRIS pH 5.5, 25%w/v polyethylene glycol, 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.84	33.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.607	α = 90
b = 42.655	β = 116.82
c = 61.289	γ = 90

Symmetry
Space Group	C 1 2 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		2008-08-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.9786	APS	21-ID-G

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	2.1	50	98.8	0.07	0.07	21.5	2.5	14965	14965		-3	31.9

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	2.1	2.14	99.6		0.405	0.405	2.5	2.5	734

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	3DLO	2.1	50	14059	14059	738	98.78	0.2017	0.2017	0.1997	0.2041	0.23747	0.2421	RANDOM	38.86

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]
-0.1		-1.35	0.63		-1.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.469
r_dihedral_angle_4_deg	15.662
r_dihedral_angle_3_deg	15.158
r_dihedral_angle_1_deg	5.673
r_angle_refined_deg	1.425
r_angle_other_deg	0.84
r_chiral_restr	0.081
r_bond_refined_d	0.014
r_bond_other_d	0.006
r_gen_planes_refined	0.005
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1970
Nucleic Acid Atoms
Solvent Atoms	50
Heterogen Atoms	34

Software

Software
Software Name	Purpose
MD2	data collection
HKL-3000	phasing
MOLREP	phasing
REFMAC	refinement
Coot	model building
HKL-3000	data reduction
HKL-3000	data scaling