6TRH | pdb_00006trh

Structure of E70A mutant of Rex8A from Paenibacillus barcinonensis complexed with 3(3)-alpha-L-arabinofuranosyl-xylotetraose.

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	20% PEG 3350, 0.2M Potassium thiocyanate, 0.1M Bis Tris propane pH 7.5. Microseeding. Co-crystallization: 5 mM 3(3)-alpha-L-arabinofuranosyl-xylotetraose. Cryoprotectant: 25% Glycerol.

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.295	α = 90
b = 82.72	β = 90
c = 465.317	γ = 90

Symmetry
Space Group	C 2 2 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 6M	KB Mirrors	2019-10-20	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	1.85	46.62	97.2	0.153	0.162	0.052	0.992	8	7.4		129847

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	1.86	1.89	80.7		0.658	0.768	0.377	0.568	1	3.2

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	6SRD	1.86	46.62	123280	6472	95.69	0.2398	0.2385	0.24	0.2633	0.26	RANDOM	33.218

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]
-8.51			-6.95		15.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.423
r_dihedral_angle_3_deg	14.792
r_dihedral_angle_4_deg	13.273
r_dihedral_angle_1_deg	6.66
r_angle_refined_deg	1.417
r_angle_other_deg	1.24
r_chiral_restr	0.081
r_bond_refined_d	0.006
r_bond_other_d	0.004
r_gen_planes_refined	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.423
r_dihedral_angle_3_deg	14.792
r_dihedral_angle_4_deg	13.273
r_dihedral_angle_1_deg	6.66
r_angle_refined_deg	1.417
r_angle_other_deg	1.24
r_chiral_restr	0.081
r_bond_refined_d	0.006
r_bond_other_d	0.004
r_gen_planes_refined	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12535
Nucleic Acid Atoms
Solvent Atoms	194
Heterogen Atoms	184

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
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.