4X47 | pdb_00004x47

Crystal structure of the intramolecular trans-sialidase from Ruminococcus gnavus in complex with Neu5Ac2en

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	microseeding into 0.8 M NaH2PO4, 1.2M K2HPO4, sodium acetate 0.1M pH 4.5

Crystal Properties
Matthews coefficient	Solvent content
2.41	49.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.305	α = 90
b = 101.305	β = 90
c = 131.939	γ = 120

Symmetry
Space Group	H 3

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		2014-08-14	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	45	99.5	0.064	15.3	2.9		33968

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	2.03	99.7		0.49		2.6	1743

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2sli	2	45	32166	1586	98.82	0.2174	0.2146	0.22	0.2728	0.28	RANDOM	40.44

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]
1.11	0.56		1.11		-3.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.393
r_dihedral_angle_3_deg	16.035
r_dihedral_angle_4_deg	12.596
r_dihedral_angle_1_deg	7.526
r_mcangle_it	4.544
r_mcbond_it	3.481
r_mcbond_other	3.481
r_angle_refined_deg	1.787
r_angle_other_deg	0.829
r_chiral_restr	0.103

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.393
r_dihedral_angle_3_deg	16.035
r_dihedral_angle_4_deg	12.596
r_dihedral_angle_1_deg	7.526
r_mcangle_it	4.544
r_mcbond_it	3.481
r_mcbond_other	3.481
r_angle_refined_deg	1.787
r_angle_other_deg	0.829
r_chiral_restr	0.103
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3803
Nucleic Acid Atoms
Solvent Atoms	235
Heterogen Atoms	25

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
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.