3DDV | pdb_00003ddv

The crystal structure of the transcriptional regulator (GntR family) from Enterococcus faecalis V583

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	289	0.1M Tris, 2M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.87	68.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.153	α = 90
b = 86.153	β = 90
c = 240.059	γ = 120

Symmetry
Space Group	P 32 2 1

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 315	mirrors	2007-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9794	APS	19-ID

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	2.65	80.06	98.1	0.124	47.9	13.4	29406	28847	2	2	52

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	2.65	2.718	75.68		0.643	1.88	8.9	2253

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	SAD	THROUGHOUT	2.65	80.06	29406	28847	1529	98.1	0.20828	0.20609	0.22	0.25115	0.26	RANDOM	51.144

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]
0.22	0.11		0.22		-0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.183
r_dihedral_angle_4_deg	20.32
r_dihedral_angle_3_deg	19.695
r_dihedral_angle_1_deg	8.379
r_scangle_it	3.064
r_scbond_it	2.063
r_angle_refined_deg	2.008
r_mcangle_it	1.429
r_mcbond_it	1.165
r_angle_other_deg	1.021
r_symmetry_hbond_refined	0.386
r_symmetry_vdw_refined	0.248
r_nbd_refined	0.233
r_symmetry_vdw_other	0.221
r_nbd_other	0.212
r_nbtor_refined	0.202
r_xyhbond_nbd_refined	0.189
r_mcbond_other	0.156
r_chiral_restr	0.11
r_nbtor_other	0.099
r_xyhbond_nbd_other	0.056
r_bond_refined_d	0.02
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4185
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing