2F5T | pdb_00002f5t

Crystal Structure of the sugar binding domain of the archaeal transcriptional regulator TrmB

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	291	100mM sodium acetate, 8%(w/v) PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.857	α = 90
b = 56.857	β = 90
c = 132.482	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						M	SINGLE WAVELENGTH
2	1
3	1
4	1
5	1
6	1
7	1
8	1
9	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.85, 0.978, 0.979, 1.699	SLS	X06SA

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	1.45	39.53	97.2	0.049	36.1			44046

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	1.45	1.54	87.5		0.29	8.12		55823

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MIRAS	THROUGHOUT	1.45	39.53	43989	2224	98.7	0.164	0.162	0.16	0.195	0.19	RANDOM	16.215

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]
0.05	0.02		0.05		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.578
r_dihedral_angle_4_deg	16.826
r_dihedral_angle_3_deg	12.483
r_dihedral_angle_1_deg	11.865
r_sphericity_free	9.977
r_sphericity_bonded	5.659
r_scangle_it	5.169
r_scbond_it	3.745
r_mcangle_it	2.703
r_rigid_bond_restr	2.197
r_mcbond_it	1.956
r_angle_refined_deg	1.822
r_nbtor_refined	0.32
r_chiral_restr	0.298
r_nbd_refined	0.221
r_symmetry_vdw_refined	0.194
r_symmetry_hbond_refined	0.128
r_xyhbond_nbd_refined	0.116
r_bond_refined_d	0.017
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1878
Nucleic Acid Atoms
Solvent Atoms	105
Heterogen Atoms	28

Software

Software
Software Name	Purpose
XSCALE	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction