3IB3 | pdb_00003ib3

Crystal Structure of SACOL2612 - CocE/NonD family hydrolase from Staphylococcus aureus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3III

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	293	suberic acid, sebacic acid, hexadecanedioic acid, dodecanedioic acid 12mM each, PEG3350 20%, Hepes 0.1M pH 7.5, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.221	α = 90
b = 160.583	β = 90
c = 216.827	γ = 90

Symmetry
Space Group	C 2 2 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	ADSC QUANTUM 315r	Mirror	2008-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9786	APS	19-ID

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	2.05	50	99.3	0.156	0.156	16	7.2	72687	72687		-3

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	2.05	2.09	86.8		0.554	0.554	2.7	5.4	3155

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	3III	2.05	50	68929	68929	3653	99.61	0.19351	0.19351	0.1905	0.2	0.24951	0.26	RANDOM	8.07

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]
0.3			-3.74		3.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.134
r_dihedral_angle_4_deg	17.244
r_dihedral_angle_3_deg	14.2
r_dihedral_angle_1_deg	7.162
r_scangle_it	3.226
r_scbond_it	2.306
r_angle_other_deg	2.227
r_angle_refined_deg	1.595
r_mcangle_it	1.207
r_mcbond_it	0.728
r_mcbond_other	0.122
r_chiral_restr	0.1
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_gen_planes_other	0.004
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8937
Nucleic Acid Atoms
Solvent Atoms	726
Heterogen Atoms	10

Software

Software
Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
REFMAC	refinement
Coot	model building
HKL-2000	data reduction
HKL-2000	data scaling