8BDP | pdb_00008bdp

A GH20 family sulfoglycosidase Bt4394 in complex with NAG-thiazoline and sulfite

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3RCN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	PROTEIN STOCK AT 45 MG/ML IN THE REMARK 280 BUFFER OF 50 MM NAPO4 AND 500 MM NACL IS MIXED WITH THE REMARK 280 PRECIPITANT OF 0.2 M KSCN, 21% PEG3350, 0.1 M BIS-TRIS PROPANE REMARK 280 PH 6.5, AT A RATIO OF 1.2: 1.

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.832	α = 90
b = 60.785	β = 107.905
c = 74.223	γ = 90

Symmetry
Space Group	P 1 21 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		2019-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.979183	SSRF	BL19U1

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	1.47	70.63	95.4	0.997	7.8	1.9		91859

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	1.47	1.5	65		0.624	1.1	1.9

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	3rcn	1.47	70.628	91840	4641	95.312	0.133	0.1299	0.13	0.1823	0.18	23.43

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]
0.883		1.716	-0.916		-0.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.437
r_dihedral_angle_3_deg	13.23
r_dihedral_angle_1_deg	6.467
r_scangle_it	5.969
r_scangle_other	5.968
r_dihedral_angle_2_deg	5.662
r_lrange_it	5.587
r_lrange_other	5.481
r_scbond_it	5.326
r_scbond_other	5.326
r_rigid_bond_restr	5.063
r_mcangle_other	4.023
r_mcangle_it	4.019
r_mcbond_it	3.549
r_mcbond_other	3.549
r_angle_refined_deg	1.559
r_angle_other_deg	0.547
r_nbd_refined	0.223
r_nbd_other	0.197
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.18
r_symmetry_nbd_refined	0.162
r_symmetry_xyhbond_nbd_refined	0.159
r_xyhbond_nbd_refined	0.15
r_symmetry_xyhbond_nbd_other	0.126
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.078
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4252
Nucleic Acid Atoms
Solvent Atoms	457
Heterogen Atoms	1

Software

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