5HNN

Crystal structure of the endo-beta-1,4-glucanase (Xac0030) from Xanthomonas axonopodis pv. citri with the triple mutation His174Trp, Tyr211Ala and Lys227Arg.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	32% PEG4000 0.2 M sodium chloride 0.1 M Tris

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.554	α = 90
b = 76.87	β = 98.7
c = 128.942	γ = 90

Symmetry
Space Group	P 1 21 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 2M		2014-09-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.458	LNLS	W01B-MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.63	41.48	93.8	0.044	15.05	2.78		110097		-3	20.272

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.63	1.73	83.6		0.307	2.31

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4W7U	1.63	41.47	104633	5522	93.82	0.1488	0.1462	0.1976	RANDOM	21.303

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]
0.07		-0.08			-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.233
r_sphericity_free	28.163
r_dihedral_angle_4_deg	19.737
r_dihedral_angle_3_deg	13.289
r_sphericity_bonded	8.581
r_dihedral_angle_1_deg	6.137
r_mcangle_it	2.243
r_mcbond_it	1.732
r_mcbond_other	1.729
r_angle_refined_deg	1.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.233
r_sphericity_free	28.163
r_dihedral_angle_4_deg	19.737
r_dihedral_angle_3_deg	13.289
r_sphericity_bonded	8.581
r_dihedral_angle_1_deg	6.137
r_mcangle_it	2.243
r_mcbond_it	1.732
r_mcbond_other	1.729
r_angle_refined_deg	1.33
r_rigid_bond_restr	1.272
r_angle_other_deg	0.943
r_chiral_restr	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7408
Nucleic Acid Atoms
Solvent Atoms	581
Heterogen Atoms	24

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.