7KV3 | pdb_00007kv3

Surface glycan-binding protein A from Bacteroides thetaiotaomicron in complex with laminarihexaose

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		295	0.1 M bis-tris pH 6.5, 0.2 M lithium sulfate, 25 % (w/v) PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.024	α = 90
b = 72.937	β = 105.644
c = 101.484	γ = 90

Symmetry
Space Group	I 1 2 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	PIXEL	DECTRIS PILATUS3 6M		2020-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97946	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.05	39.45	99	0.992	8	7		33221

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.11			0.668

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	2.05	39.447	33221	1639	98.778	0.159	0.1569	0.17	0.2041	0.21	20.868

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]
0.815		-0.473	-0.018		-0.461

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.043
r_dihedral_angle_4_deg	18.266
r_dihedral_angle_3_deg	13.593
r_dihedral_angle_1_deg	6.586
r_lrange_it	4.617
r_lrange_other	4.583
r_scangle_it	3.628
r_scangle_other	3.624
r_angle_other_deg	2.682
r_mcangle_other	2.61
r_mcangle_it	2.609
r_scbond_it	2.304
r_scbond_other	2.302
r_mcbond_it	1.744
r_mcbond_other	1.741
r_angle_refined_deg	1.516
r_nbd_other	0.248
r_symmetry_nbd_refined	0.24
r_symmetry_nbd_other	0.211
r_nbd_refined	0.197
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.156
r_symmetry_xyhbond_nbd_refined	0.124
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.077
r_bond_other_d	0.036
r_gen_planes_other	0.012
r_bond_refined_d	0.009
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3793
Nucleic Acid Atoms
Solvent Atoms	295
Heterogen Atoms	72

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing