6XQG | pdb_00006xqg

Crystal structure of SCLam E144S mutant, a non-specific endo-beta-1,3(4)-glucanase from family GH16, co-crystallized with 1,3-beta-D-cellobiosyl-cellobiose, presenting a 1,3-beta-D-cellobiosyl-glucose at active site

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6XOF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	30 % PEG4000, 0.1 M MgCl, and 0.1 M Tris

Crystal Properties
Matthews coefficient	Solvent content
1.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.73	α = 90
b = 48.97	β = 90
c = 114.27	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 PILATUS 2M		2015-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.4586	LNLS	W01B-MX2

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	2.15	45.01	100	0.179	0.198	0.082	0.967	5.4	5.8		12437

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	2.15	2.22	100		0.822	0.926	0.417	0.465		5.3

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	6XOF	2.15	45.01	11788	602	99.96	0.1856	0.1826	0.19	0.2438	0.25	RANDOM	26.528

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]
-0.28			1.62		-1.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.438
r_dihedral_angle_4_deg	21.723
r_dihedral_angle_3_deg	13.786
r_dihedral_angle_1_deg	8.361
r_angle_refined_deg	1.828
r_angle_other_deg	1.365
r_chiral_restr	0.077
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.438
r_dihedral_angle_4_deg	21.723
r_dihedral_angle_3_deg	13.786
r_dihedral_angle_1_deg	8.361
r_angle_refined_deg	1.828
r_angle_other_deg	1.365
r_chiral_restr	0.077
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1941
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms	35

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
iMOSFLM	data reduction

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.