2Z2N

Crystal Structure of selenomethionine substituted virginiamycin B lyase from Staphylococcus aureus

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	100mM phosphate citrate buffer (pH 4.2), 15%(w/v) PEG 8000, 10-17%(v/v) PEG 500MME, 175mM NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.85	33.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.97	α = 90
b = 34.752	β = 117.86
c = 86.601	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	95	CCD	ADSC QUANTUM 4		2004-01-01	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X8C	0.9000, 0.9798, 1.0600	NSLS	X8C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.65	50	96.7	0.038	18.5	7.5		29320

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.75	78.2		0.383	3.7	6

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	1.65	20	25084	2747	93.28	0.16092	0.15604	0.20309	RANDOM	20.205

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]
-0.18		-1.77	-1.43		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.671
r_dihedral_angle_4_deg	20.475
r_dihedral_angle_3_deg	17.132
r_dihedral_angle_1_deg	9.109
r_scangle_it	4.239
r_scbond_it	3.291
r_angle_refined_deg	2.271
r_mcangle_it	2.1
r_mcbond_it	1.656
r_angle_other_deg	1.125
r_mcbond_other	0.449
r_symmetry_hbond_refined	0.38
r_symmetry_vdw_other	0.255
r_nbd_refined	0.254
r_xyhbond_nbd_refined	0.252
r_nbd_other	0.216
r_symmetry_vdw_refined	0.207
r_nbtor_refined	0.192
r_chiral_restr	0.165
r_nbtor_other	0.095
r_bond_refined_d	0.025
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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	2272
Nucleic Acid Atoms
Solvent Atoms	210
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SnB	phasing
BEAST	phasing