3POH | pdb_00003poh

Crystal structure of an endo-beta-N-acetylglucosaminidase (BT_3987) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.55 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	1.0M NaCitrate, 0.1M Imidazole pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.449	α = 90
b = 74.449	β = 90
c = 133.913	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	CCD	ADSC QUANTUM 315		2010-10-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.9537,0.9795,0.9793	ALS	8.2.2

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	1.55	29.712	99.3	0.051	17.76			62783		-3	16.663

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	1.55	1.61	94.1		0.357	2.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.55	29.712	62730	3178	99.52	0.1375	0.1361	0.15	0.1636	0.18	RANDOM	23.5834

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]
0.34	0.17		0.34		-0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.445
r_dihedral_angle_4_deg	16.035
r_dihedral_angle_3_deg	11.471
r_dihedral_angle_1_deg	6.078
r_scangle_it	5.558
r_scbond_it	3.66
r_mcangle_it	2.436
r_mcbond_it	1.523
r_angle_refined_deg	1.511
r_angle_other_deg	0.927

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.445
r_dihedral_angle_4_deg	16.035
r_dihedral_angle_3_deg	11.471
r_dihedral_angle_1_deg	6.078
r_scangle_it	5.558
r_scbond_it	3.66
r_mcangle_it	2.436
r_mcbond_it	1.523
r_angle_refined_deg	1.511
r_angle_other_deg	0.927
r_mcbond_other	0.45
r_chiral_restr	0.098
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3325
Nucleic Acid Atoms
Solvent Atoms	612
Heterogen Atoms	5

Software

Software
Software Name	Purpose
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	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.