9GUJ | pdb_00009guj

Crystal structure of transcription factor NtcA from Synechococcus elongatus in complex with its transcriptional co- activator PipX and its target DNA (Crystal II)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		model composed by one NtcA dimer, one DNA double helical molecule and one PipX molecule

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294.15	PipX-NtcA-DNA complex was in 50 mM sodium citrate pH 6.5, 0.5 M NaCl, 5 mM magnesium cloride, 50 mM arginine hydrocloride, 50 mM Na L-glutamate and 10mM 2-oxoglutarate. CRYSTALLIZATION SOLUTION: 0,1M Tris-HCL pH 8,5, 2M ammonium phosphate and 0,1M ZnCl2. Cryo protectant: 4M KCL

Crystal Properties
Matthews coefficient	Solvent content
3.6	65.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 165.71	α = 90
b = 165.71	β = 90
c = 177.55	γ = 90

Symmetry
Space Group	I 4

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		2011-09-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9772	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	4.3	82.9	98.5	0.074	4.8	3.8		16116

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	4.3	4.53			0.472

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	MOLECULAR REPLACEMENT	THROUGHOUT	4.3	82.86	15313	802	98.46	0.28528	0.28357	0.2757	0.31614	0.3147	RANDOM	91.929

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]
35.59			35.59		-71.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	19.64
r_dihedral_angle_2_deg	9.128
r_dihedral_angle_1_deg	5.763
r_angle_refined_deg	1.614
r_angle_other_deg	0.447
r_chiral_restr	0.101
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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	8809
Nucleic Acid Atoms	2419
Solvent Atoms
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
XDS	data reduction
PHASER	phasing