8J9F | pdb_00008j9f

Structure of STG-hydrolyzing beta-glucosidase 1 (PSTG1)

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	PEG 3000, imidazole, lithium sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.3	62.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.3	α = 71.468
b = 113.25	β = 82.684
c = 158.66	γ = 79.83

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	80	PIXEL	DECTRIS EIGER X 9M		2021-06-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL32XU	1.0	SPring-8	BL32XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	2.85	50	99.6	0.619	0.879	3.65	8.46		832650

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.85	3.02	99.8		1.661	0.515	1.33	8.25

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.85	47.6	98461	5067	99.681	0.234	0.2317	0.23	0.2817	0.28	Random selection	19.839

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]
-1.229	-0.629	-0.115	1.792	1.404	-0.033

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.764
r_dihedral_angle_3_deg	17.346
r_dihedral_angle_1_deg	6.043
r_lrange_it	5.639
r_lrange_other	5.638
r_dihedral_angle_2_deg	3.645
r_scangle_it	2.955
r_scangle_other	2.955
r_mcangle_it	2.696
r_mcangle_other	2.696
r_scbond_it	1.702
r_scbond_other	1.702
r_angle_refined_deg	1.648
r_mcbond_it	1.592
r_mcbond_other	1.592
r_angle_other_deg	0.856
r_nbd_other	0.244
r_symmetry_nbd_refined	0.243
r_symmetry_nbd_other	0.233
r_nbd_refined	0.212
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.186
r_ncsr_local_group_2	0.125
r_ncsr_local_group_5	0.125
r_ncsr_local_group_4	0.123
r_ncsr_local_group_3	0.122
r_ncsr_local_group_1	0.12
r_ncsr_local_group_6	0.12
r_symmetry_xyhbond_nbd_refined	0.115
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.072
r_symmetry_xyhbond_nbd_other	0.067
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_gen_planes_other	0.005
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	23104
Nucleic Acid Atoms
Solvent Atoms	491
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing