7UZ1 | pdb_00007uz1

Structure of beta-glycosidase from Sulfolobus solfataricus in complex with C5a-bromo-valienide.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1UWR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295	10 - 13 % PEG 4000, 0.1 M Sodium Acetate, 0.2M Ammonium Acetate, 5% ethylene glycol.

Crystal Properties
Matthews coefficient	Solvent content
3.43	64.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 168.088	α = 90
b = 168.088	β = 90
c = 95.548	γ = 120

Symmetry
Space Group	P 31 2 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 EIGER X 16M		2021-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.033	APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.58	46.4	99.9	0.025	1	12.2	10.1		211061

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.58	1.62	100		0.805	0.37	0.7

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	1UWR	1.58	43.301	211023	10231	99.868	0.19	0.1894	0.2	0.2123	0.22	33.763

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]
-0.345	-0.173		-0.345		1.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.173
r_dihedral_angle_4_deg	16.775
r_dihedral_angle_3_deg	14.512
r_dihedral_angle_1_deg	6.956
r_lrange_it	6.55
r_lrange_other	6.548
r_scangle_it	5.712
r_scangle_other	5.711
r_scbond_it	4.072
r_scbond_other	4.072
r_mcangle_other	3.701
r_mcangle_it	3.699
r_mcbond_it	3.031
r_mcbond_other	3.028
r_angle_refined_deg	1.906
r_angle_other_deg	1.502
r_nbd_other	0.229
r_nbd_refined	0.209
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.181
r_symmetry_nbd_refined	0.175
r_xyhbond_nbd_refined	0.12
r_symmetry_xyhbond_nbd_refined	0.099
r_chiral_restr	0.097
r_symmetry_nbtor_other	0.087
r_bond_refined_d	0.013
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7941
Nucleic Acid Atoms
Solvent Atoms	392
Heterogen Atoms	28

Software

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