4MDY

Crystal structure of periplasmic solute binding protein from Mycobacterium smegmatis str. MC2 155

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	289	0.2M Sodium Citrate, 0.1 M Phosphate-citrate, 20 % PEG 8000, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.606	α = 90
b = 90.449	β = 90
c = 33.974	γ = 90

Symmetry
Space Group	P 21 21 2

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 315r		2012-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97899	APS	19-ID

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	1.78	50	97.3	0.091	23.1	6.9	25588	24908		-3

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	1.78	1.81	97.3		0.992	1.92	6.1	1170

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.78	31.82	22242	22242	1113	87.12	0.149	0.149	0.1463	0.2005	RANDOM	25.3141

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]
-0.64			-1.75		2.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.033
r_sphericity_free	29.141
r_dihedral_angle_4_deg	17.577
r_dihedral_angle_3_deg	12.772
r_sphericity_bonded	8.522
r_dihedral_angle_1_deg	5.222
r_rigid_bond_restr	1.807
r_angle_refined_deg	1.068
r_angle_other_deg	0.721
r_chiral_restr	0.056

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.033
r_sphericity_free	29.141
r_dihedral_angle_4_deg	17.577
r_dihedral_angle_3_deg	12.772
r_sphericity_bonded	8.522
r_dihedral_angle_1_deg	5.222
r_rigid_bond_restr	1.807
r_angle_refined_deg	1.068
r_angle_other_deg	0.721
r_chiral_restr	0.056
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2145
Nucleic Acid Atoms
Solvent Atoms	199
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXDE	phasing
ARP/wARP	model building
RESOLVE	phasing
Coot	model building

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.