6EZT

Crystal structure of GH20 Exo beta-N-Acetylglucosaminidase D437A inactive mutant from Vibrio harveyi

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	4.5	293	0.1 M sodium acetate pH 4.6, 1.4 M sodium malonate

Crystal Properties
Matthews coefficient	Solvent content
3.61	65.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.42	α = 90
b = 129.24	β = 112.2
c = 98.36	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 6M		2012-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.97889	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.6	91.09	99.8	0.125	0.136	0.993	9.7	6.861		63617		-3	56.757

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.67	99.7		0.775	0.835	0.865	2.18	7.102

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	6EZR	2.6	91.09	60437	3180	99.9	0.197	0.1949	0.2365	RANDOM	64.279

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]
2.04		2.04	-6.58		2.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.224
r_dihedral_angle_4_deg	17.85
r_dihedral_angle_3_deg	16.379
r_dihedral_angle_1_deg	5.693
r_angle_refined_deg	1.21
r_angle_other_deg	0.907
r_chiral_restr	0.065
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.224
r_dihedral_angle_4_deg	17.85
r_dihedral_angle_3_deg	16.379
r_dihedral_angle_1_deg	5.693
r_angle_refined_deg	1.21
r_angle_other_deg	0.907
r_chiral_restr	0.065
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10280
Nucleic Acid Atoms
Solvent Atoms	426
Heterogen Atoms	40

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building
REFMAC	refinement
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 R01GM133198.