6ER4

Ruminococcus gnavus IT-sialidase CBM40 bound to alpha2,6 sialyllactose

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M ammonium chloride with 20% PEG 8000 crystal growth time was improved using micro-seeding Crystals were cryoprotected using the crystallisation condition supplemented with 25% (w/w) glycerol crystal was co-crystallised with 10mM 2,6 sialyllactose and soaked with 100mM 2,6 sialyllactose immediately prior to freezing

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.74	α = 90
b = 72.2	β = 103.88
c = 51.41	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+		2014-07-17	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 Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.3	49.91	83.9	0.031	0.034	0.013	32	5.1		70604

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.303	1.34	13.6		0.148	0.148	0.143	5.5	1.4

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	1.3	49.91	67097	3481	83.8	0.1097	0.1084	0.1345	RANDOM	11.479

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]
0.48		-0.37	-0.16		-0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.246
r_sphericity_free	31.802
r_dihedral_angle_4_deg	19.417
r_dihedral_angle_3_deg	11.265
r_sphericity_bonded	7.215
r_dihedral_angle_1_deg	7.193
r_rigid_bond_restr	2.375
r_angle_refined_deg	1.712
r_angle_other_deg	1.65
r_mcangle_it	1.034
r_mcbond_it	0.771
r_mcbond_other	0.765
r_chiral_restr	0.115
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.008
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2896
Nucleic Acid Atoms
Solvent Atoms	488
Heterogen Atoms	123

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction