4GNV

Crystal structure of beta-hexosaminidase 1 from Burkholderia cenocepacia J2315 with bound N-Acetyl-D-Glucosamine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289	EBS Internal tracking number 234629b12: BuceA.18451.a.B1.PW36254 at 20 mg/mL in 25 mM HEPES (pH 7.0), 500 mM NaCl, 2 mM DTT, 0.025% Sodium Azide, 5% glycerol. 0.4 uL x 0.4 uL drop with Morpheus Screen B12: 90 mM Halogens (NaF, NaBr, NaI), 0.1 M Tris/Bicine pH 8.5, 37.5% MPD-PEG1000-PEG3500, SOAK 1 week with 10 mM N-acetyl-D-glucosamine, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.97	α = 90
b = 89.31	β = 91.73
c = 67.15	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	CCD	ADSC QUANTUM 315		2012-06-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	0.976484	ALS	5.0.3

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	1.5	67.12	97.8	0.041	28.22	6.11	551832	85727

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	1.5	1.539	84.57		0.229	4.57

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.5	67.12	90246	4519	97.82	0.1493	0.1479	0.1755	RANDOM	14.266

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]
0.05		-0.06	0.63		-0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.545
r_dihedral_angle_4_deg	17.248
r_dihedral_angle_3_deg	12.564
r_dihedral_angle_1_deg	5.895
r_angle_refined_deg	1.456
r_angle_other_deg	0.93
r_chiral_restr	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.545
r_dihedral_angle_4_deg	17.248
r_dihedral_angle_3_deg	12.564
r_dihedral_angle_1_deg	5.895
r_angle_refined_deg	1.456
r_angle_other_deg	0.93
r_chiral_restr	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5102
Nucleic Acid Atoms
Solvent Atoms	630
Heterogen Atoms	34

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.