4GHJ | pdb_00004ghj

1.75 Angstrom Crystal Structure of Transcriptional Regulator ftom Vibrio vulnificus.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	295	Protein: 7.6mg/mL, 0.5M Sodium cloride, 0.01M Tris-HCl pH 8.3; Screen: PACT (D6), 0.1M MMT buffer pH 9.0, 25% (w/v) PEG 1500, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.76	29.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.742	α = 90
b = 70.74	β = 90
c = 35.746	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	100	CCD	MARMOSAIC 300 mm CCD	Beryllium lenses	2012-07-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	1.75	30	97.6	0.095	31.3	6.9	16622	16622		-3	21.7

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	1.75	1.78	83.6		0.482	3.3	5.8	713

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	SAD	THROUGHOUT	1.75	28.53	15662	15662	847	97.5	0.18366	0.18366	0.18157	0.1961	0.22341	0.234	RANDOM	21.626

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]
-2.88			4.4		-1.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.073
r_dihedral_angle_4_deg	12.816
r_dihedral_angle_3_deg	9.897
r_scangle_it	5.193
r_scbond_it	3.176
r_dihedral_angle_1_deg	2.887
r_mcangle_it	1.904
r_angle_refined_deg	1.227
r_mcbond_it	1.158
r_angle_other_deg	0.811

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.073
r_dihedral_angle_4_deg	12.816
r_dihedral_angle_3_deg	9.897
r_scangle_it	5.193
r_scbond_it	3.176
r_dihedral_angle_1_deg	2.887
r_mcangle_it	1.904
r_angle_refined_deg	1.227
r_mcbond_it	1.158
r_angle_other_deg	0.811
r_mcbond_other	0.398
r_chiral_restr	0.077
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1148
Nucleic Acid Atoms
Solvent Atoms	149
Heterogen Atoms

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	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.