6QWI | pdb_00006qwi

Structure of beta-glucosidase A from Paenibacillus polymyxa complexed with multivalent inhibitors.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E4I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	13% (v/v) PEG 3350, 0.2M sodium nitrate, 3% 2-Methyl-2,4-pentanediol (MPD) and 0.1 M BisTris propane, pH 7.5 and 0.56 mM 6-Cyclohexylhexyl beta-D-maltoside. Cryoprotectant mother liquor supplemented with 25% glycerol.

Crystal Properties
Matthews coefficient	Solvent content
3.64	66.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 146.096	α = 90
b = 146.096	β = 90
c = 140.345	γ = 90

Symmetry
Space Group	P 4 21 2

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 PILATUS3 S 6M	KB focusing mirrors	2018-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979260	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	48.7	76.4	0.141	0.151	0.052	0.985	10.3	7.8		27295			45.005

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.85	3	79.1		0.689	0.737	0.252	0.804	2.8	7.7

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1E4I	2.85	48.52	25865	1405	75.55	0.18315	0.18056	0.19	0.23128	0.24	RANDOM	43.586

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]
-0.42			-0.42		0.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.087
r_dihedral_angle_4_deg	21.54
r_dihedral_angle_3_deg	16.423
r_long_range_B_refined	6.566
r_long_range_B_other	6.562
r_dihedral_angle_1_deg	6.426
r_scangle_other	4.292
r_mcangle_it	3.911
r_mcangle_other	3.911
r_scbond_it	2.622
r_scbond_other	2.622
r_mcbond_it	2.486
r_mcbond_other	2.472
r_angle_refined_deg	1.381
r_angle_other_deg	1.259
r_chiral_restr	0.058
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7294
Nucleic Acid Atoms
Solvent Atoms	150
Heterogen Atoms	50

Software

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