3PNT | pdb_00003pnt

Crystal Structure of the Streptococcus pyogenes NAD+ glycohydrolase SPN in complex with IFS, the Immunity Factor for SPN

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	PEG 8000, NaCl, Tris (8.0), vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 198.817	α = 90
b = 57.892	β = 107.2
c = 89.699	γ = 90

Symmetry
Space Group	C 1 2 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	NOIR-1			M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	0.97892, 0.97938, 0.99510	ALS	4.2.2

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	2.8	42.72				24375	24309

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	MAD	THROUGHOUT	2.8	42.72	23069	1240	99.73	0.21166	0.20802	0.2157	0.27811	0.2804	RANDOM	17.832

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]
-0.01		-0.03	-0.08		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.996
r_dihedral_angle_4_deg	20.413
r_dihedral_angle_3_deg	19.322
r_dihedral_angle_1_deg	6.453
r_scangle_it	1.746
r_angle_refined_deg	1.193
r_scbond_it	1.081
r_angle_other_deg	0.827
r_mcangle_it	0.652
r_mcbond_it	0.328

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.996
r_dihedral_angle_4_deg	20.413
r_dihedral_angle_3_deg	19.322
r_dihedral_angle_1_deg	6.453
r_scangle_it	1.746
r_angle_refined_deg	1.193
r_scbond_it	1.081
r_angle_other_deg	0.827
r_mcangle_it	0.652
r_mcbond_it	0.328
r_chiral_restr	0.066
r_mcbond_other	0.049
r_bond_refined_d	0.01
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	6640
Nucleic Acid Atoms
Solvent Atoms	153
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

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.