4XVV

Crystal structure of an Acid stress chaperone HdeB (KPN_03484) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.70 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	277	0.2M ammonium sulfate, 30.0% polyethylene glycol monomethyl ether 2000, 0.1M sodium acetate pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
1.98	38.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.475	α = 90
b = 39.443	β = 90
c = 98.256	γ = 90

Symmetry
Space Group	P 21 21 21

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	KOHZU: Double Crystal Si(111)	2014-10-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.979559	ALS	8.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.7	29.286	95.4	0.052	0.069	9.32	3.62		15930		-3	29.463

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	1.7	1.76	94.4		0.708	0.948	1.6

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.7	29.286	15888	808	97.77	0.198	0.1966	0.2261	RANDOM	33.9187

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]
-0.42			0.49		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.897
r_dihedral_angle_4_deg	24.547
r_dihedral_angle_3_deg	13.73
r_dihedral_angle_1_deg	4.777
r_mcangle_it	2.681
r_mcbond_it	1.711
r_mcbond_other	1.7
r_angle_refined_deg	1.377
r_angle_other_deg	1.124
r_chiral_restr	0.085

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.897
r_dihedral_angle_4_deg	24.547
r_dihedral_angle_3_deg	13.73
r_dihedral_angle_1_deg	4.777
r_mcangle_it	2.681
r_mcbond_it	1.711
r_mcbond_other	1.7
r_angle_refined_deg	1.377
r_angle_other_deg	1.124
r_chiral_restr	0.085
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1178
Nucleic Acid Atoms
Solvent Atoms	76
Heterogen Atoms

Software

Software
Software Name	Purpose
PDB_EXTRACT	data extraction
SOLVE	phasing
XSCALE	data scaling
REFMAC	refinement

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.