3K11

Crystal structure of Putative glycosyl hydrolase (NP_813087.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.80 A resolution

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	5.0000% PEG-6000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.81	67.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.135	α = 90
b = 121.135	β = 90
c = 182.812	γ = 120

Symmetry
Space Group	P 63 2 2

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	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2009-05-15	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162,0.97936,0.97919	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.8	29.988	100	0.101	0.101	14.3	7.3		73725			22.138

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.85	100		0.764	0.764	1	7.3	5333

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	MAD	THROUGHOUT	1.8	29.988	73676	3714	99.96	0.151	0.15	0.171	RANDOM	29.571

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]
1.61	0.81		1.61		-2.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.443
r_dihedral_angle_4_deg	22.615
r_dihedral_angle_3_deg	12.368
r_scangle_it	6.089
r_dihedral_angle_1_deg	5.038
r_scbond_it	4.819
r_mcangle_it	2.535
r_mcbond_it	1.988
r_angle_refined_deg	1.544
r_angle_other_deg	1.08
r_mcbond_other	0.549
r_symmetry_vdw_refined	0.241
r_symmetry_vdw_other	0.239
r_nbd_refined	0.225
r_symmetry_hbond_refined	0.193
r_nbtor_refined	0.191
r_nbd_other	0.185
r_xyhbond_nbd_refined	0.178
r_chiral_restr	0.101
r_nbtor_other	0.089
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3489
Nucleic Acid Atoms
Solvent Atoms	468
Heterogen Atoms	88

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHARP	phasing