7KV5 | pdb_00007kv5

Surface glycan-binding protein B from Bacteroides fluxus

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		295	0.1 M MES pH6.6, 0.2 M ammonium sulfate, 20 % (w/v) PEG5000MME 0.1 M guanidine hydrochloride

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.533	α = 90
b = 77.619	β = 90
c = 146.621	γ = 90

Symmetry
Space Group	I 2 2 2

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 BL9-2	0.97946	SSRL	BL9-2

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	1.82	39.71	99.7	0.999	12.3	6.6		30831

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	1.82	1.86			0.934

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	1.82	39.709	30831	1532	99.683	0.193	0.1909	0.2	0.2301	0.24	31.74

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]
-1.527			5.096		-3.569

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.022
r_dihedral_angle_4_deg	17.565
r_dihedral_angle_3_deg	11.623
r_dihedral_angle_1_deg	7.558
r_lrange_it	5.876
r_lrange_other	5.875
r_scangle_it	4.559
r_scangle_other	4.557
r_scbond_it	3.283
r_scbond_other	3.281
r_mcangle_other	3.251
r_mcangle_it	3.25
r_mcbond_it	2.445
r_angle_other_deg	2.443
r_mcbond_other	2.44
r_angle_refined_deg	1.555
r_symmetry_xyhbond_nbd_refined	0.219
r_symmetry_nbd_other	0.216
r_nbd_refined	0.198
r_xyhbond_nbd_refined	0.187
r_nbtor_refined	0.172
r_nbd_other	0.161
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.069
r_symmetry_nbd_refined	0.065
r_bond_other_d	0.037
r_dihedral_angle_other_2_deg	0.026
r_gen_planes_other	0.011
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_symmetry_xyhbond_nbd_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1851
Nucleic Acid Atoms
Solvent Atoms	324
Heterogen Atoms	30

Software

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