7SV6

Crystal structure of SpaA-SLH/G46A/G109A in complex with 4,6-Pyr-beta-D-ManNAc-(1->4)-beta-D-GlcNAcOMe

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6CWM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291.15	0.1 M sodium acetate, 25% (w/v) PEG 4000, 8% (w/v) isopropanol

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.303	α = 90
b = 65.611	β = 90
c = 72.29	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 200K		2019-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.85	20	98.2	0.099	0.113	0.053	8.1	4.3		13823

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.92	99.3		0.54	0.646	0.345	0.795		3.2

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	6CWM	1.85	19.63	13083	694	97.74	0.1877	0.1861	0.2173	RANDOM	21.533

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]
2.21			-0.86		-1.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.091
r_dihedral_angle_4_deg	11.914
r_dihedral_angle_3_deg	11.875
r_dihedral_angle_1_deg	5.617
r_angle_other_deg	1.27
r_angle_refined_deg	1.228
r_chiral_restr	0.052
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.091
r_dihedral_angle_4_deg	11.914
r_dihedral_angle_3_deg	11.875
r_dihedral_angle_1_deg	5.617
r_angle_other_deg	1.27
r_angle_refined_deg	1.228
r_chiral_restr	0.052
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1268
Nucleic Acid Atoms
Solvent Atoms	112
Heterogen Atoms	35

Software

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

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.