2OGG | pdb_00002ogg

Structure of B. subtilis trehalose repressor (TreR) effector binding domain

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	Reservoir: 0.1M MES pH 6.0, 1.26M Ammonium sulfate, 0.56mM CYMAL-5. Protein: 21.2mg/ml. Drops: 1+1 microliter, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.98	69.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.719	α = 90
b = 69.719	β = 90
c = 236.535	γ = 90

Symmetry
Space Group	I 41 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	MARRESEARCH		2006-10-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97900	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	2.5	50	95.6	0.06	50	6		10126			58.7

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	2.5	2.54	70.5		0.278	3.2	3.9

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	2.5	37.88	10126	10126	990	95.64	0.19576	0.19576	0.19024	0.19	0.24659	0.24	RANDOM	43.687

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]
-0.71			-0.71		1.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.337
r_dihedral_angle_3_deg	17.082
r_dihedral_angle_4_deg	14.926
r_scangle_it	9.32
r_scbond_it	7.027
r_dihedral_angle_1_deg	6.938
r_mcangle_it	3.73
r_mcbond_it	2.28
r_angle_refined_deg	1.412
r_chiral_restr	0.358
r_nbtor_refined	0.337
r_nbd_refined	0.281
r_symmetry_vdw_refined	0.264
r_symmetry_hbond_refined	0.173
r_xyhbond_nbd_refined	0.159
r_gen_planes_refined	0.025
r_bond_refined_d	0.013
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1213
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms	29

Software

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