2QX2 | pdb_00002qx2

Structure of the C-terminal domain of sex pheromone staph-cAM373 precursor from Staphylococcus aureus

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	15% Ethanol, 0.1M Tris-HCl pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.976	α = 90
b = 69.976	β = 90
c = 145.954	γ = 120

Symmetry
Space Group	P 32 1 2

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 315		2006-07-09	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97932, 0.97943	APS	19-ID

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	1.9	50	90.2	0.087	8.2	8.8	29466	29466		-3	28.4

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	1.9	1.97	57		0.427	0.427	2.1	4.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.9	34.99	27918	27918	1499	90.25	0.18318	0.18318	0.18138	0.2062	0.21701	0.2321	RANDOM	41.548

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]
-2.2	-1.1		-2.2		3.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.903
r_dihedral_angle_4_deg	18.433
r_dihedral_angle_3_deg	13.159
r_dihedral_angle_1_deg	5.854
r_scangle_it	3.152
r_scbond_it	2.086
r_angle_refined_deg	1.301
r_mcangle_it	1.224
r_mcbond_it	0.81
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.903
r_dihedral_angle_4_deg	18.433
r_dihedral_angle_3_deg	13.159
r_dihedral_angle_1_deg	5.854
r_scangle_it	3.152
r_scbond_it	2.086
r_angle_refined_deg	1.301
r_mcangle_it	1.224
r_mcbond_it	0.81
r_nbtor_refined	0.302
r_nbd_refined	0.208
r_symmetry_hbond_refined	0.181
r_symmetry_vdw_refined	0.176
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.085
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2571
Nucleic Acid Atoms
Solvent Atoms	338
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.