3V4G

1.60 Angstrom resolution crystal structure of an arginine repressor from Vibrio vulnificus CMCP6

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	295	protein: 7.3 mg/mL in 10 mM Tris-HCl pH 8.3, 0.25 M NaCl, 5 mM BME. Crystallization: The Classics II Suite (A9: 0.1 M Bis-Tris pH 5.5, 3 M NaCl). Cryo: 5M NaCl+50% sucrose, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.308	α = 90
b = 73.308	β = 90
c = 118.597	γ = 120

Symmetry
Space Group	P 63 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	MARMOSAIC 300 mm CCD	mirror	2011-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97903	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	1.6	30	100	0.063	38.3	14	25607	25607		-3	21.1

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	1.6	1.63	100		0.514	6.25	14.3	1242

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1XXB and 1F9N	1.6	29.65	24257	24257	1300	99.96	0.18246	0.18164	0.19787	RANDOM	23.941

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]
-0.83	-0.41		-0.83		1.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	22.386
r_dihedral_angle_4_deg	12.64
r_dihedral_angle_3_deg	5.87
r_scangle_it	3.408
r_scbond_it	2.021
r_angle_refined_deg	1.602
r_dihedral_angle_1_deg	1.521
r_mcangle_it	1.244
r_angle_other_deg	0.936
r_mcbond_it	0.649

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	22.386
r_dihedral_angle_4_deg	12.64
r_dihedral_angle_3_deg	5.87
r_scangle_it	3.408
r_scbond_it	2.021
r_angle_refined_deg	1.602
r_dihedral_angle_1_deg	1.521
r_mcangle_it	1.244
r_angle_other_deg	0.936
r_mcbond_it	0.649
r_mcbond_other	0.152
r_chiral_restr	0.094
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1118
Nucleic Acid Atoms
Solvent Atoms	176
Heterogen Atoms

Software

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

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 R01GM133198.