3CED | pdb_00003ced

Crystal structure of the C-terminal NIL domain of an ABC transporter protein homologue from Staphylococcus aureus

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	289	20% 1,4-Butanediol, 0.1M Acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
4.39	71.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.55	α = 90
b = 132.55	β = 90
c = 132.083	γ = 90

Symmetry
Space Group	I 4 2 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		2008-02-07	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9793, 0.9795	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	2.15	50	99.9	0.087	8.2	16.3	32344	32344		-3	36.2

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	2.15	2.2	100		0.463	2.4	16.5	2279

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	2.15	35.4	32204	32204	1632	99.92	0.186	0.186	0.184	0.1808	0.215	0.2104	RANDOM	37.948

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]
-0.42			-0.42		0.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.234
r_dihedral_angle_3_deg	13.902
r_dihedral_angle_4_deg	9.389
r_dihedral_angle_1_deg	6.032
r_scangle_it	3.968
r_scbond_it	2.418
r_mcangle_it	1.567
r_angle_refined_deg	1.303
r_mcbond_it	1.106
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.234
r_dihedral_angle_3_deg	13.902
r_dihedral_angle_4_deg	9.389
r_dihedral_angle_1_deg	6.032
r_scangle_it	3.968
r_scbond_it	2.418
r_mcangle_it	1.567
r_angle_refined_deg	1.303
r_mcbond_it	1.106
r_nbtor_refined	0.302
r_symmetry_vdw_refined	0.232
r_nbd_refined	0.192
r_xyhbond_nbd_refined	0.121
r_symmetry_hbond_refined	0.114
r_chiral_restr	0.101
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2316
Nucleic Acid Atoms
Solvent Atoms	323
Heterogen Atoms	24

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
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.