4EJO | pdb_00004ejo

Crystal structure of padr family transcriptional regulator from Eggerthella lenta DSM 2243

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	277	0.1M PHOSPHATE-CITRATE PH 4.2, 40% ETHANOL, 5% PEG 1000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE, temperature 277 K

Crystal Properties
Matthews coefficient	Solvent content
1.83	32.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.783	α = 90
b = 55.783	β = 90
c = 132.425	γ = 90

Symmetry
Space Group	I 41

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 315r		2010-10-11	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97948, 0.97959	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	2.1	50	100	0.126	33.9	9.6	11881	11880		-3

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	2.1	2.12	100		0.542	4	8.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.1	50	11854	532	99.77	0.1833	0.181	0.1802	0.2353	0.2092	RANDOM	44.9808

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]
15.51			15.51		-31.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.889
r_sphericity_free	29.428
r_sphericity_bonded	28.29
r_dihedral_angle_4_deg	19.055
r_dihedral_angle_3_deg	17.921
r_dihedral_angle_1_deg	6.941
r_rigid_bond_restr	5.435
r_angle_refined_deg	1.667
r_chiral_restr	0.104
r_bond_refined_d	0.013
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1767
Nucleic Acid Atoms
Solvent Atoms	22
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXDE	phasing
RESOLVE	phasing
ARP/wARP	model building