5F9T

Crystal Structure of Streptococcus pneumoniae NanC, covalent complex with a fluorinated Neu5Ac derivative

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VW2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	16% PEG8000, 20% glycerol, 40mM monopotassium phosphate, 10% sugar free Irn Bru

Crystal Properties
Matthews coefficient	Solvent content
2.86	56.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.236	α = 90
b = 74.843	β = 96.31
c = 113.352	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	CCD	RIGAKU SATURN 944+		2013-09-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54178

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	2.05	30	97.7	0.107	9.1	3.5		102205

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	2.05	2.09	75.1		0.576		2.8	3930

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	2vw2	2.05	30	96897	5098	97.37	0.1995	0.1976	0.2348	RANDOM	33.251

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]
0.79		-0.1	0.25		-1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.24
r_dihedral_angle_3_deg	13.524
r_dihedral_angle_4_deg	10.65
r_dihedral_angle_1_deg	7.32
r_mcangle_it	5.7
r_mcbond_it	5.307
r_mcbond_other	5.307
r_angle_refined_deg	1.433
r_angle_other_deg	1.094
r_chiral_restr	0.081

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.24
r_dihedral_angle_3_deg	13.524
r_dihedral_angle_4_deg	10.65
r_dihedral_angle_1_deg	7.32
r_mcangle_it	5.7
r_mcbond_it	5.307
r_mcbond_other	5.307
r_angle_refined_deg	1.433
r_angle_other_deg	1.094
r_chiral_restr	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.005
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10444
Nucleic Acid Atoms
Solvent Atoms	553
Heterogen Atoms	92

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction
Coot	model building

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.