4X6K

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

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 1.2 M NaH2PO4, 0.8 M K2HPO4, 0.1 M CAPS pH 10.5

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.109	α = 90
b = 99.109	β = 90
c = 131.708	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		2014-09-25	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	1.94	50	98.3	0.066	14.5	3.1		34757

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	1.94	1.97	97.7		0.458		3	1678

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	2sli	1.94	71.91	1586	97.5	0.1793	0.177	0.225	RANDOM	27.04

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]
0.54	0.27		0.54		-1.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.068
r_dihedral_angle_3_deg	13.524
r_dihedral_angle_4_deg	12.547
r_dihedral_angle_1_deg	7.491
r_mcangle_it	2.879
r_mcbond_it	2.234
r_mcbond_other	2.234
r_angle_refined_deg	1.898
r_angle_other_deg	0.87
r_chiral_restr	0.117

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.068
r_dihedral_angle_3_deg	13.524
r_dihedral_angle_4_deg	12.547
r_dihedral_angle_1_deg	7.491
r_mcangle_it	2.879
r_mcbond_it	2.234
r_mcbond_other	2.234
r_angle_refined_deg	1.898
r_angle_other_deg	0.87
r_chiral_restr	0.117
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3778
Nucleic Acid Atoms
Solvent Atoms	465
Heterogen Atoms	18

Software

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

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.