3KZ9 | pdb_00003kz9

Crystal structure of the master transcriptional regulator, SmcR, in Vibrio vulnificus provides insight into its DNA recognition mechanism

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	294	0.2M Lithium sulfate, 7% PEG 3000, 0.1M imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.494	α = 90
b = 99.025	β = 90
c = 129.06	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	ADSC QUANTUM 210		2006-09-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 6C1	1.23985	PAL/PLS	6C1

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	2.1	35	99.2	0.072	0.047	26.97	6.9	59111	56004	2	2

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	2.1	2.18	95.6		0.475	0.393	3.28	6.2	5617

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	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	SAD	THROUGHOUT	2.1	29.92	2	2	59111	56004	2979	99.16	0.212	0.20033	0.19759	0.1985	0.25095	0.251	RANDOM	35.58

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]
-1.94			2.63		-0.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.816
r_dihedral_angle_4_deg	16.911
r_dihedral_angle_3_deg	16.342
r_dihedral_angle_1_deg	5.284
r_scangle_it	3.629
r_scbond_it	2.471
r_mcangle_it	1.484
r_angle_refined_deg	1.329
r_mcbond_it	0.978
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.816
r_dihedral_angle_4_deg	16.911
r_dihedral_angle_3_deg	16.342
r_dihedral_angle_1_deg	5.284
r_scangle_it	3.629
r_scbond_it	2.471
r_mcangle_it	1.484
r_angle_refined_deg	1.329
r_mcbond_it	0.978
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.282
r_nbd_refined	0.207
r_xyhbond_nbd_refined	0.185
r_symmetry_hbond_refined	0.172
r_chiral_restr	0.092
r_bond_refined_d	0.014
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6560
Nucleic Acid Atoms
Solvent Atoms	453
Heterogen Atoms	30

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	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 R01GM157729.