2P5L | pdb_00002p5l

Crystal structure of a dimer of N-terminal domains of AhrC in complex with an 18bp DNA operator site

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2P5K	N-TERMINAL DOMAIN OF AHRC (2P5K) AND 7BP OF DNA FROM THE PURINE REPRESSOR-OPERATOR COMPLEX (1JFS)
experimental model	PDB	1JFS	N-TERMINAL DOMAIN OF AHRC (2P5K) AND 7BP OF DNA FROM THE PURINE REPRESSOR-OPERATOR COMPLEX (1JFS)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.1	277	1.7M ammonium sulphate, 0.1M HEPES, 0.1M sodium chloride, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 7.10

Crystal Properties
Matthews coefficient	Solvent content
4.77	74.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.105	α = 90
b = 118.77	β = 90
c = 121.23	γ = 90

Symmetry
Space Group	I 21 21 21

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 4	MIRRORS	2003-10-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.2		SRS	PX14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.85	24.81	98	0.063	0.063	18	4.1		23191			75.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.85	3	98		0.406	0.406	3.4	4.1

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	N-TERMINAL DOMAIN OF AHRC (2P5K) AND 7BP OF DNA FROM THE PURINE REPRESSOR-OPERATOR COMPLEX (1JFS)	2.85	24.81	23191	1198	97.5	0.208	0.207	0.196	0.231	0.2155	RANDOM	23.9

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]
-0.89			0.53		0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.998
r_dihedral_angle_4_deg	23.381
r_dihedral_angle_3_deg	18.637
r_dihedral_angle_1_deg	5.263
r_angle_refined_deg	1.675
r_mcangle_it	1.173
r_scangle_it	0.874
r_mcbond_it	0.695
r_scbond_it	0.587
r_nbtor_refined	0.346
r_symmetry_vdw_refined	0.344
r_nbd_refined	0.251
r_symmetry_hbond_refined	0.246
r_xyhbond_nbd_refined	0.211
r_chiral_restr	0.069
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
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	2064
Nucleic Acid Atoms	1448
Solvent Atoms	13
Heterogen Atoms	25

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing