3S3T | pdb_00003s3t

Universal stress protein UspA from Lactobacillus plantarum

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	0.2 M calcium acetate, 0.1 M Tris buffer, 20% PEG-3000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.015	α = 102.13
b = 56.187	β = 100.53
c = 109.144	γ = 90.36

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	SBC-3		2008-08-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.9792	APS	19-BM

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	1.9	32.5	92.9	0.073	8.5	6.2	81926	81926			35

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	1.9	1.93	62		0.561	2.85	6.1	2729

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	2ZSK	1.9	32.5	81918	81918	4103	92.69	0.171	0.171	0.1684	0.17	0.2207	0.22	RANDOM	29.2979

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]
-0.95	-0.34	0.73	-0.72	-1.67	1.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.218
r_dihedral_angle_4_deg	20.452
r_dihedral_angle_3_deg	13.237
r_dihedral_angle_1_deg	6.22
r_scangle_it	3.37
r_scbond_it	2.186
r_angle_refined_deg	1.662
r_mcangle_it	1.344
r_angle_other_deg	0.955
r_mcbond_it	0.798

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.218
r_dihedral_angle_4_deg	20.452
r_dihedral_angle_3_deg	13.237
r_dihedral_angle_1_deg	6.22
r_scangle_it	3.37
r_scbond_it	2.186
r_angle_refined_deg	1.662
r_mcangle_it	1.344
r_angle_other_deg	0.955
r_mcbond_it	0.798
r_mcbond_other	0.256
r_chiral_restr	0.093
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8800
Nucleic Acid Atoms
Solvent Atoms	886
Heterogen Atoms	308

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-2000	data reduction
HKL-3000	data scaling
MOLREP	phasing
HKL-3000	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.