3GEU | pdb_00003geu

Crystal Structure of IcaR from Staphylococcus aureus, a member of the tetracycline repressor protein family

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	298	PEG3350 20%, 0.2M NH4 Formate, pH 7, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.922	α = 90
b = 121.141	β = 90
c = 61.686	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	MARMOSAIC 300 mm CCD		2008-12-05	M	SINGLE WAVELENGTH
2	1	x-ray	110	CCD	MARMOSAIC 300 mm CCD		2009-02-08	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97624	APS	21-ID-D
2	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.990	APS	21-ID-D

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	1.9	50	99.3	0.08		7.6	67790	67319	1.6	2.4

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	1.9	1.97	93.7		0.474	2.4	4.3	6284

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	1.9	40.42	67790	67217	3392	98.81	0.184	0.182	0.183	0.228	0.2284	RANDOM	35.916

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]
0.27			0.11		-0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.176
r_dihedral_angle_4_deg	25.252
r_dihedral_angle_3_deg	15.193
r_scangle_it	10.234
r_scbond_it	7.331
r_dihedral_angle_1_deg	5.258
r_mcangle_it	4.802
r_mcbond_it	3.339
r_angle_refined_deg	1.501
r_nbtor_refined	0.326

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.176
r_dihedral_angle_4_deg	25.252
r_dihedral_angle_3_deg	15.193
r_scangle_it	10.234
r_scbond_it	7.331
r_dihedral_angle_1_deg	5.258
r_mcangle_it	4.802
r_mcbond_it	3.339
r_angle_refined_deg	1.501
r_nbtor_refined	0.326
r_symmetry_vdw_refined	0.277
r_symmetry_hbond_refined	0.267
r_nbd_refined	0.255
r_xyhbond_nbd_refined	0.181
r_chiral_restr	0.107
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6280
Nucleic Acid Atoms
Solvent Atoms	431
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
BLU-MAX	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing

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.