3D02

Crystal structure of periplasmic sugar-binding protein (YP_001338366.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.30 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	277	1.00M LiCl, 30.00% PEG-6000, 0.1M Citrate pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.24	α = 90
b = 76.96	β = 90
c = 113.98	γ = 90

Symmetry
Space Group	C 2 2 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	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2008-03-16	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162,0.97932,0.97918	SSRL	BL9-2

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	1.3	28.63	96.5	0.042	11.43			70966		-3	10.873

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	1.3	1.35	84.9		0.405	2

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	MAD	THROUGHOUT	1.3	28.63	70928	3596	99.13	0.158	0.157	0.172	RANDOM	10.239

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]
0.26			0.05		-0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.325
r_dihedral_angle_4_deg	14.926
r_dihedral_angle_3_deg	11.254
r_scangle_it	5.926
r_dihedral_angle_1_deg	5.597
r_scbond_it	4.001
r_mcangle_it	2.325
r_angle_refined_deg	1.767
r_mcbond_it	1.412
r_angle_other_deg	1.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.325
r_dihedral_angle_4_deg	14.926
r_dihedral_angle_3_deg	11.254
r_scangle_it	5.926
r_dihedral_angle_1_deg	5.597
r_scbond_it	4.001
r_mcangle_it	2.325
r_angle_refined_deg	1.767
r_mcbond_it	1.412
r_angle_other_deg	1.009
r_mcbond_other	0.411
r_chiral_restr	0.103
r_bond_refined_d	0.018
r_gen_planes_refined	0.011
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2263
Nucleic Acid Atoms
Solvent Atoms	313
Heterogen Atoms	9

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	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 R01GM133198.