3JQ0

Crystal structure of SusD superfamily protein (YP_001299712.1) from Bacteroides vulgatus ATCC 8482 at 1.13 A resolution

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	1.60M (NH4)2SO4, 0.1M TRIS pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.804	α = 90
b = 75.804	β = 90
c = 323.966	γ = 120

Symmetry
Space Group	P 65 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 mirror, vertical and horizontal focussing mirrors	2009-05-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2		SSRL	BL12-2

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	1.13	29.45	91.5	0.111	0.111	9.3	5		187091			7.466

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	1.13	1.16	58.1		0.58	0.58	1.3	3.6	8584

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	SAD	THROUGHOUT	1.13	29.45	187080	9433	90.93	0.118	0.117	0.137	RANDOM	13.075

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]
0.16	0.08		0.16		-0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.015
r_dihedral_angle_4_deg	15.435
r_dihedral_angle_3_deg	11.578
r_sphericity_free	9.239
r_dihedral_angle_1_deg	6.113
r_scangle_it	4.421
r_sphericity_bonded	3.897
r_scbond_it	3.213
r_mcangle_it	2.206
r_angle_refined_deg	1.673
r_mcbond_it	1.553
r_rigid_bond_restr	1.529
r_angle_other_deg	1.013
r_mcbond_other	0.732
r_chiral_restr	0.112
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3866
Nucleic Acid Atoms
Solvent Atoms	833
Heterogen Atoms	48

Software

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