2JEU | pdb_00002jeu

Transcription activator structure reveals redox control of a replication initiation reaction

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DTO	PDB ENTRY 1DTO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5		PROTEIN WAS CRYSTALLISED FROM 0.1 M TRIS-HCL PH 8.5, 0.3 M NACL AND 18-22% TERTIARY BUTANOL, USING THE HANGING DROP METHOD OF VAPOUR DIFFUSION.

Crystal Properties
Matthews coefficient	Solvent content
2.71	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.539	α = 90
b = 61.539	β = 90
c = 236.317	γ = 120

Symmetry
Space Group	P 61 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	120	CCD	ADSC CCD		2004-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1		ESRF	ID14-1

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	2.8	25	99.2	0.06	32	7.3		7171		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	2.8	2.9	92.1		0.5	3.5	5.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1DTO	2.8	24.33	6594	500	100	0.236	0.233	0.23	0.281	RANDOM	78.02

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]
-3.01	-1.5		-3.01		4.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.296
r_dihedral_angle_3_deg	16.991
r_dihedral_angle_4_deg	9.164
r_dihedral_angle_1_deg	5.616
r_scangle_it	2.438
r_scbond_it	1.45
r_angle_refined_deg	1.018
r_mcangle_it	0.89
r_mcbond_it	0.441
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.246
r_nbd_refined	0.203
r_xyhbond_nbd_refined	0.131
r_symmetry_hbond_refined	0.117
r_chiral_restr	0.07
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1578
Nucleic Acid Atoms
Solvent Atoms	17
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing