6R4K | pdb_00006r4k

Structure of beta-glucosidase A from Paenibacillus polymyxa complexed with a monovalent inhibitor

X-RAY DIFFRACTION

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	18% (v/v) PEG 3350, 0.2M sodium nitrate, 3% 2-Methyl-2,4-pentanediol (MPD), 0.1 M Bis-Tris propane, pH 7.5, and 5% n-Dodecyl beta-D-maltoside. Cryoprotectant mother liquor supplemented with 25% glycerol.

Crystal Properties
Matthews coefficient	Solvent content
3.65	66.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 146.725	α = 90
b = 146.725	β = 90
c = 140.055	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	2018-07-22	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	2.13	48.91	99.9	0.104	0.113	0.043	0.991	11.6	6.7		85545

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	2.13	2.17	99.6		0.701	0.765	0.299	0.655	2.2	6.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1E4I	2.13	48.646	83	85512	4518	99.82	0.2175	0.2159	0.23	0.2413	0.26

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	7.746
f_angle_d	1.2
f_chiral_restr	0.065
f_bond_d	0.01
f_plane_restr	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7294
Nucleic Acid Atoms
Solvent Atoms	458
Heterogen Atoms	56

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.