4X4A

Crystal structure of the intramolecular trans-sialidase from Ruminococcus gnavus in complex with 2,7-Anhydro-Neu5Ac

X-RAY DIFFRACTION

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.257	α = 90
b = 99.257	β = 90
c = 130.599	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		2014-08-27	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	1.71	45	92.9	0.049	20	4.2		48126

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	1.71	1.74	53		0.421		2.4	1358

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.71	45	45702	2250	92.54	0.1454	0.1432	0.1884	RANDOM	29.958

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]
0.73	0.36		0.73		-2.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.169
r_dihedral_angle_4_deg	18.251
r_dihedral_angle_3_deg	12.388
r_dihedral_angle_1_deg	7.781
r_mcangle_it	3.238
r_mcbond_it	2.516
r_mcbond_other	2.515
r_angle_refined_deg	1.891
r_angle_other_deg	0.883
r_chiral_restr	0.122

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.169
r_dihedral_angle_4_deg	18.251
r_dihedral_angle_3_deg	12.388
r_dihedral_angle_1_deg	7.781
r_mcangle_it	3.238
r_mcbond_it	2.516
r_mcbond_other	2.515
r_angle_refined_deg	1.891
r_angle_other_deg	0.883
r_chiral_restr	0.122
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3779
Nucleic Acid Atoms
Solvent Atoms	529
Heterogen Atoms	46

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 R01GM133198.