4HS7 | pdb_00004hs7

2.6 Angstrom Structure of the Extracellular Solute-binding Protein from Staphylococcus aureus in complex with PEG.

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	295	Protein: 7.4mg/mL, 0.25M Sodium cloride, 0.01M Tris-HCl pH 8.3; Screen: JCSG+ (B12), 0.2M tri-Potassium citrate pH 8.3, 20% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3	58.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.863	α = 90
b = 101.863	β = 90
c = 191.341	γ = 120

Symmetry
Space Group	P 65

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 225 mm CCD	Beryllium lenses	2012-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	2.6	30	98.8	0.09	17.7	5.4	34117	34117		-3	57.5

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	2.6	2.64	99.6		0.644	3	5.4	1701

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	PDB ENTRY 2ZYO	2.6	29.99	32393	32393	1721	98.99	0.17003	0.17003	0.16742	0.17	0.21933	0.21	RANDOM	39.585

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]
3.05	1.52		3.05		-4.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.756
r_dihedral_angle_3_deg	11.515
r_dihedral_angle_4_deg	10.949
r_scangle_it	5.358
r_scbond_it	3.393
r_dihedral_angle_1_deg	2.885
r_mcangle_it	1.979
r_angle_refined_deg	1.37
r_mcbond_it	1.044
r_angle_other_deg	0.805

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.756
r_dihedral_angle_3_deg	11.515
r_dihedral_angle_4_deg	10.949
r_scangle_it	5.358
r_scbond_it	3.393
r_dihedral_angle_1_deg	2.885
r_mcangle_it	1.979
r_angle_refined_deg	1.37
r_mcbond_it	1.044
r_angle_other_deg	0.805
r_mcbond_other	0.246
r_chiral_restr	0.083
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6032
Nucleic Acid Atoms
Solvent Atoms	291
Heterogen Atoms	60

Software

Software
Software Name	Purpose
Blu-Ice	data collection
BALBES	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

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.