6XQF | pdb_00006xqf

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-cellotriosyl-glucose, 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, 0.2 M magnesium chloride, and 0.1 M Tris

Crystal Properties
Matthews coefficient	Solvent content
1.85	33.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.692	α = 90
b = 49.868	β = 90
c = 114.474	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		2015-03-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.4583	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	1.58	45.72	97.2	0.084	0.094	0.042	0.989	13.9	5		30357

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	1.58	1.61	77.7		0.367	0.447	0.247	0.631		2.9

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	1.58	45.72	28544	1487	96.26	0.1733	0.1714	0.18	0.2089	0.22	RANDOM	10.568

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]
-0.6			0.1		0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.913
r_dihedral_angle_4_deg	16.066
r_dihedral_angle_3_deg	11.91
r_dihedral_angle_1_deg	8.093
r_angle_refined_deg	1.941
r_angle_other_deg	1.554
r_chiral_restr	0.097
r_bond_refined_d	0.016
r_gen_planes_refined	0.013
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.913
r_dihedral_angle_4_deg	16.066
r_dihedral_angle_3_deg	11.91
r_dihedral_angle_1_deg	8.093
r_angle_refined_deg	1.941
r_angle_other_deg	1.554
r_chiral_restr	0.097
r_bond_refined_d	0.016
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2023
Nucleic Acid Atoms
Solvent Atoms	455
Heterogen Atoms	35

Software

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

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.