5SUO | pdb_00005suo

Crystal structure of N-glycan transport solute binding protein (NgtS) from Streptococcus pneumoniae

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	29 % PEG 1500, 11 % 2-methyl-2,4-pentanediol, 0.1 M Tris

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.91	α = 90
b = 40.2	β = 98.77
c = 93.89	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++		2013-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-002	1.54187

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.73	92.79	99.9	25.4	4.7		25262

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.1	92.79	25262	1339	99.73	0.2136	0.211	0.2114	0.2611	0.2617	RANDOM	19.711

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]
0.03			0.02		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.726
r_dihedral_angle_4_deg	22.699
r_dihedral_angle_3_deg	15.302
r_dihedral_angle_1_deg	5.959
r_mcangle_it	1.865
r_angle_refined_deg	1.418
r_scbond_it	1.268
r_mcbond_it	1.101
r_chiral_restr	0.091
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3486
Nucleic Acid Atoms
Solvent Atoms	227
Heterogen Atoms	21

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction