8BAL

Niako3494, a bacterial protein structure in glycoside hydrolase family 20

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	Protein stock at 18mg/mL, in the precipitant: 0.1 M MMT buffer (DL-Malic acid, MES monohydrate, Tris base [ratio 1:2:2]), pH 6.0, 25 % w/v PEG 1500, protein to precipitant ratio 1:1, 1 uL drop size, +50 nL 1:10000 diluted seed stock. Cryoprotectant used was made up with 20% PEG400 in 80% mother liquor.

Crystal Properties
Matthews coefficient	Solvent content
3	58.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 146.987	α = 90
b = 254.589	β = 90
c = 139.58	γ = 90

Symmetry
Space Group	C 2 2 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 EIGER2 XE 16M		2022-04-29	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	2.27	73.49	99.9	0.958	6.3	13.9		120442

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	2.27	2.31	99.1		0.336	1.1	13.6

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	Alphafold	2.27	73.49	120411	6125	99.939	0.287	0.2828	0.3561	31.39

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]
6.14			7.703		-13.844

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	20.057
r_dihedral_angle_6_deg	14.829
r_dihedral_angle_1_deg	11.394
r_dihedral_angle_2_deg	10.329
r_lrange_it	5.836
r_lrange_other	5.836
r_mcangle_it	4.12
r_mcangle_other	4.12
r_scangle_it	3.202
r_scangle_other	3.202
r_mcbond_it	2.802
r_mcbond_other	2.802
r_scbond_it	2.176
r_scbond_other	2.176
r_angle_refined_deg	1.613
r_angle_other_deg	0.515
r_symmetry_xyhbond_nbd_refined	0.347
r_metal_ion_refined	0.342
r_xyhbond_nbd_refined	0.29
r_nbd_refined	0.288
r_symmetry_nbd_refined	0.237
r_symmetry_nbd_other	0.234
r_xyhbond_nbd_other	0.203
r_nbd_other	0.201
r_nbtor_refined	0.198
r_symmetry_xyhbond_nbd_other	0.106
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.071
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13710
Nucleic Acid Atoms
Solvent Atoms	28
Heterogen Atoms	5

Software

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