Experiment: 5DPN

Engineered CBM X-2 L110F in complex with branched carbohydrate XXXG.

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4BJ0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	Large crystals were grown in 9-well glass plates using Hampton sandwich box set-up.

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.977	α = 90
b = 49.856	β = 90
c = 45.091	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
2	1	neutron	293	IMAGE PLATE	FUJI		2014-11-25	M	SINGLE WAVELENGTH
1	1	x-ray	100	CCD	MAR CCD 165 mm		2014-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
2	NUCLEAR REACTOR	FRM II BEAMLINE BIODIFF	2.66	FRM II	BIODIFF
1	SYNCHROTRON	MAX II BEAMLINE I911-2	1.04	MAX II	I911-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	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
2	1.6	45	91.1	0.041						6.6	3		20530
1	1.6	29.3	97.7	0.093						28.6	5.5		21610

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.7		0.231						7.8	5.5	3389
2	1.6	1.65		0.449						1.8	2.5	1485

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1.6	45				20512	1027	91.09		0.2239	0.2225	0.1664	0.25	0.2072
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	1.606	29.445				21609	1081	97.69		0.1648	0.1628		0.204

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	22.277
f_dihedral_angle_d	22.277
f_angle_d	1.268
f_angle_d	1.268
f_chiral_restr	0.08
f_chiral_restr	0.08
f_bond_d	0.01
f_bond_d	0.01
f_plane_restr	0.006
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1260
Nucleic Acid Atoms
Solvent Atoms	60
Heterogen Atoms	73
Protein Atoms	1260
Nucleic Acid Atoms
Solvent Atoms	60
Heterogen Atoms	73

Software

Software
Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
Coot	model building

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.