3CAG | pdb_00003cag

Crystal structure of the oligomerization domain hexamer of the arginine repressor protein from Mycobacterium tuberculosis in complex with 9 arginines.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ZFZ	PDB entry 2ZFZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	12% PEG 10000, 0.1M Hepes pH 7.0, 0.2M L-arginine, 10% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.745	α = 90
b = 75.648	β = 90
c = 108.022	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	100	CCD	MARMOSAIC 225 mm CCD		2007-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	1.10552	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.9	50	95.6	0.132	0.132	15.7	6.9	36125	36125

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	84.6		0.422	0.422	4.2	6.8	3141

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2ZFZ	1.9	42.26	34288	1793	95.37	0.17083	0.16813	0.17	0.22414	0.17	RANDOM	23.608

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]
-0.7			1.78		-1.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.849
r_dihedral_angle_3_deg	15.528
r_dihedral_angle_4_deg	15.397
r_dihedral_angle_1_deg	5.776
r_scangle_it	4.057
r_scbond_it	2.616
r_angle_refined_deg	1.483
r_mcangle_it	1.432
r_mcbond_it	0.96
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.849
r_dihedral_angle_3_deg	15.528
r_dihedral_angle_4_deg	15.397
r_dihedral_angle_1_deg	5.776
r_scangle_it	4.057
r_scbond_it	2.616
r_angle_refined_deg	1.483
r_mcangle_it	1.432
r_mcbond_it	0.96
r_nbtor_refined	0.301
r_nbd_refined	0.217
r_symmetry_hbond_refined	0.178
r_xyhbond_nbd_refined	0.153
r_symmetry_vdw_refined	0.146
r_chiral_restr	0.099
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3393
Nucleic Acid Atoms
Solvent Atoms	357
Heterogen Atoms	108

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	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.