6TO0 | pdb_00006to0

Structure of E70A mutant of Rex8A from Paenibacillus barcinonensis complexed with 2(3)-alpha-L-arabinofuranosyl-xylotriose.

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	18% PEG 3350, 0.2M Potassium thiocyanate, 0.1M Bis-Tris propane pH 7.5. Microseeding. Co-crystallization with 2(3)-alpha-L-arabinofuranosyl-xylotriose

Crystal Properties
Matthews coefficient	Solvent content
3.53	65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.9	α = 90
b = 87.9	β = 90
c = 274.18	γ = 120

Symmetry
Space Group	P 31 2 1

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	1.88	44.53	99.9	0.078	0.085	0.032	0.998	13.8	6.5		100926

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	1.88	1.91	99.5		0.609	0.66	0.357	0.92

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	1.88	44.53	95555	5276	99.87	0.2355	0.2343	0.24	0.2573	0.27	RANDOM	27.956

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]
1.21	0.61		1.21		-3.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.461
r_dihedral_angle_4_deg	15.105
r_dihedral_angle_3_deg	13.056
r_dihedral_angle_1_deg	6.593
r_angle_refined_deg	1.474
r_angle_other_deg	1.429
r_chiral_restr	0.077
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.461
r_dihedral_angle_4_deg	15.105
r_dihedral_angle_3_deg	13.056
r_dihedral_angle_1_deg	6.593
r_angle_refined_deg	1.474
r_angle_other_deg	1.429
r_chiral_restr	0.077
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6248
Nucleic Acid Atoms
Solvent Atoms	423
Heterogen Atoms	86

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.