4WED

Crystal structure of ABC transporter substrate-binding protein from Sinorhizobium meliloti

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	0.2 ul of 18 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG-II condition # 18 (0.2 M Sodium Formate, 20% (w/v) PEG 3350 ) and equilibrated against 2.0 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin solution at 289 K for 3 hours.

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.327	α = 90
b = 57.327	β = 90
c = 132.063	γ = 120

Symmetry
Space Group	P 31

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	Bimorph K-B pair	2013-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.07819	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	2.35	50	97.3	0.057	0.065	0.031	15.6	4.4		19751

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.39	74.3		0.777	0.913	0.47	0.662		3.6	794

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	2.35	49.65	899	97.39	0.1667	0.1641	0.2294	RANDOM	72.611

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]
0.25	0.13		0.25		-0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.379
r_dihedral_angle_4_deg	21.54
r_dihedral_angle_3_deg	15.457
r_dihedral_angle_1_deg	6.672
r_mcangle_it	3.72
r_mcbond_other	2.551
r_mcbond_it	2.55
r_angle_refined_deg	1.541
r_angle_other_deg	0.824
r_chiral_restr	0.082

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.379
r_dihedral_angle_4_deg	21.54
r_dihedral_angle_3_deg	15.457
r_dihedral_angle_1_deg	6.672
r_mcangle_it	3.72
r_mcbond_other	2.551
r_mcbond_it	2.55
r_angle_refined_deg	1.541
r_angle_other_deg	0.824
r_chiral_restr	0.082
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3609
Nucleic Acid Atoms
Solvent Atoms	101
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
DM	phasing
MLPHARE	phasing
SHELX	phasing
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling

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.