Experiment: 7MS2

Three-dimensional structure of a GH3 Beta-glucosidase from Clostridium thermocellum in complex with glycerol

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2X40

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	0.1 M Tris-HCl:Bicine; pH 8.5; 0.12 M Alcohols [1,6-Hexanediol (HEZ), 1-buthanol (1BO), 1,2-Propanediol (PGO), 2-Propanol (IPA), 1,4-Butanediol (BU1), 1,3-Propandiol (PDO)]; 37.5% v/v Precipitant Mix [25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350]

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.84	α = 90
b = 148.06	β = 90
c = 198.64	γ = 90

Symmetry
Space Group	P 21 21 21

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 6M		2018-09-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.96863	Diamond	I24

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	2.04	69.37	99.8	0.321	0.327	0.063	0.999	7.8	26.5		120455			25.19

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	2.04	2.15	99.6		9.99	15.003	2.873	0.596		26.9

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	THROUGHOUT	2X40	2.04	60.44	1.33	69152	1999	57.33	0.2025	0.2017	0.202	0.2297	0.2295	42.6041

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	12.166
f_angle_d	0.509
f_chiral_restr	0.042
f_plane_restr	0.004
f_bond_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11327
Nucleic Acid Atoms
Solvent Atoms	405
Heterogen Atoms	40

Software

Software
Software Name	Purpose
PHENIX	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction