3K50

Crystal structure of Putative S41 protease (YP_211611.1) from Bacteroides fragilis NCTC 9343 at 2.00 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	1.0000M LiCl, 20.0000% PEG-6000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.274	α = 90
b = 91.435	β = 90
c = 107.126	γ = 90

Symmetry
Space Group	P 21 21 21

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	2009-05-14	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837,0.97936	SSRL	BL9-2

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	2	29.311	98	0.068	9.72	3.59		28549		-3	25.478

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	2	2.07	89.6		0.548	1.5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2	29.311	28503	1442	99.48	0.159	0.157	0.205	RANDOM	37.277

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]
-0.07			-1.86		1.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.479
r_dihedral_angle_4_deg	12.981
r_dihedral_angle_3_deg	12.264
r_scangle_it	6.987
r_scbond_it	5.288
r_dihedral_angle_1_deg	4.864
r_mcangle_it	3.26
r_mcbond_it	2.397
r_angle_refined_deg	1.794
r_angle_other_deg	1.08
r_mcbond_other	0.684
r_nbd_refined	0.226
r_symmetry_vdw_other	0.205
r_symmetry_hbond_refined	0.204
r_symmetry_vdw_refined	0.19
r_xyhbond_nbd_refined	0.188
r_nbtor_refined	0.186
r_nbd_other	0.184
r_chiral_restr	0.092
r_nbtor_other	0.09
r_bond_refined_d	0.019
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3035
Nucleic Acid Atoms
Solvent Atoms	317
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
autoSHARP	phasing