8BBL | pdb_00008bbl

SGL a GH20 family sulfoglycosidase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold		alphafold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	23.7 mg/mL protein in the buffer of Tris-HCl 25 mM, pH 8.0, and NaCl 200 mM was mixed 1:1 with the precipitant containing 0.1 M Bis-tris, pH 6.5, and 18-21.5% w/v PEG5000 MME.

Crystal Properties
Matthews coefficient	Solvent content
5.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.95	α = 90
b = 133.42	β = 90
c = 225.37	γ = 90

Symmetry
Space Group	P 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 EIGER2 XE 16M		2019-01-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

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	2.71	94.18	97.6	0.981	5.1	1.9		406028

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	2.71	2.77	97.8		0.343	1.6

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	alphafold	2.711	94.176	406022	20528	96.588	0.285	0.283	0.33	0.3187	0.36	25.682

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]
0.498	1.226	-6.7	-16.627	-0.939	16.129

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	20.604
r_dihedral_angle_6_deg	14.494
r_dihedral_angle_1_deg	13.098
r_dihedral_angle_2_deg	10.523
r_lrange_it	4.545
r_lrange_other	4.545
r_mcangle_it	2.928
r_mcangle_other	2.928
r_scangle_it	2.156
r_scangle_other	2.156
r_mcbond_it	1.863
r_mcbond_other	1.863
r_angle_refined_deg	1.761
r_scbond_it	1.401
r_scbond_other	1.401
r_angle_other_deg	0.587
r_nbd_other	0.37
r_symmetry_xyhbond_nbd_refined	0.351
r_symmetry_nbd_refined	0.339
r_nbd_refined	0.338
r_xyhbond_nbd_refined	0.309
r_symmetry_nbd_other	0.254
r_ncsr_local_group_4	0.248
r_ncsr_local_group_5	0.248
r_ncsr_local_group_6	0.248
r_ncsr_local_group_3	0.247
r_ncsr_local_group_1	0.246
r_ncsr_local_group_2	0.244
r_ncsr_local_group_7	0.244
r_nbtor_refined	0.204
r_ncsr_local_group_24	0.173
r_ncsr_local_group_12	0.171
r_ncsr_local_group_9	0.167
r_ncsr_local_group_21	0.167
r_ncsr_local_group_19	0.166
r_ncsr_local_group_23	0.166
r_ncsr_local_group_10	0.165
r_ncsr_local_group_26	0.165
r_ncsr_local_group_8	0.164
r_ncsr_local_group_11	0.163
r_ncsr_local_group_14	0.163
r_ncsr_local_group_15	0.163
r_ncsr_local_group_20	0.163
r_ncsr_local_group_17	0.161
r_ncsr_local_group_25	0.16
r_ncsr_local_group_16	0.158
r_ncsr_local_group_28	0.158
r_ncsr_local_group_13	0.156
r_ncsr_local_group_22	0.154
r_ncsr_local_group_27	0.153
r_symmetry_xyhbond_nbd_other	0.152
r_ncsr_local_group_18	0.15
r_symmetry_nbtor_other	0.092
r_chiral_restr	0.081
r_gen_planes_refined	0.012
r_bond_refined_d	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	31754
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing