3OYV

Crystal structure of an imelysin peptidase (BACOVA_03801) from Bacteroides ovatus ATCC 8483 at 1.25 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	277	0.05M KH2PO4, 20.00% PEG-8000, No Buffer pH 4.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.427	α = 90
b = 47.921	β = 124.62
c = 83.914	γ = 90

Symmetry
Space Group	C 1 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	MARMOSAIC 325 mm CCD		2010-05-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.85503,0.97934,0.97911	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	1.25	31.208	98.6	0.055	12.79			93405		-3	11.53

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	1.25	1.29	89.3		0.522	2.2

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	1.25	31.208	93405	4682	98.9	0.1333	0.1318	0.163	RANDOM	17.0848

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]
-0.83		-0.74	1.14		-1.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.851
r_dihedral_angle_4_deg	14.348
r_dihedral_angle_3_deg	13.301
r_sphericity_free	7.587
r_scangle_it	5.843
r_dihedral_angle_1_deg	5.309
r_sphericity_bonded	5.134
r_scbond_it	4.225
r_mcangle_it	3.173
r_mcbond_it	2.342
r_mcbond_other	2.072
r_rigid_bond_restr	1.827
r_angle_refined_deg	1.464
r_angle_other_deg	0.97
r_chiral_restr	0.09
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2756
Nucleic Acid Atoms
Solvent Atoms	533
Heterogen Atoms	19

Software

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