2Z2P

Crystal Structure of catalytically inactive H270A virginiamycin B lyase from Staphylococcus aureus with Quinupristin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Z2N	PDB ENTRY 2Z2N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		100MM MES BUFFER (PH 6.5), 20%(W/V) PEG 10000, PROTEIN SOLUTION SUPPLEMENTED WITH 3MM MGCL2, 3MM DALFOPRISTIN, 1MM QUINUPRISTIN, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.999	α = 90
b = 93.7	β = 90
c = 95.301	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	95	IMAGE PLATE	RIGAKU RAXIS IV++		2006-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300

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	2.8	50	91.1	0.136	6	4.1		14813

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	2.8	2.99	94.1		0.31	3.8	3.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2Z2N	2.8	36.18	13189	1587	91.2	0.268	0.262	0.318	RANDOM	20.33

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]
0.01			-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.518
r_dihedral_angle_3_deg	18.149
r_dihedral_angle_4_deg	11.864
r_dihedral_angle_1_deg	8.874
r_angle_refined_deg	1.512
r_scangle_it	0.972
r_mcangle_it	0.752
r_mcbond_it	0.548
r_scbond_it	0.541
r_chiral_restr	0.496
r_symmetry_hbond_refined	0.459
r_symmetry_vdw_refined	0.373
r_nbtor_refined	0.318
r_nbd_refined	0.239
r_xyhbond_nbd_refined	0.181
r_metal_ion_refined	0.152
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4662
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	120

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling