4LDV | pdb_00004ldv

Crystal structure of the DNA binding domain of A. thailana auxin response factor 1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		SeMet derivative

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.8	293	0.75 l of 4mg/mL ARF1DBD + 0.75 l crystallization buffer (2.9 M NaFormate, 0.1 M MES 6.0, 50 mM KI), pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.362	α = 90
b = 126.256	β = 90
c = 83.672	γ = 90

Symmetry
Space Group	C 2 2 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 315r		2011-06-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.97625	ESRF	ID14-4

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	39.08	98.9	0.093	7.3	3.2		81768		-3	18.4

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	1.53	99.9		0.58	1.4	2.7	11957

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	SeMet derivative	1.45	39.08	77670	4079	97.15	0.21101	0.2093	0.21	0.24344	0.24	RANDOM	18.723

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]
0.25			-0.61		0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.299
r_dihedral_angle_4_deg	17.244
r_dihedral_angle_3_deg	13.354
r_long_range_B_refined	6.954
r_dihedral_angle_1_deg	6.054
r_mcangle_it	2.394
r_scbond_it	1.716
r_angle_refined_deg	1.565
r_mcbond_it	1.413
r_chiral_restr	0.11
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
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	2591
Nucleic Acid Atoms
Solvent Atoms	298
Heterogen Atoms	23

Software

Software
Software Name	Purpose
MxCuBE	data collection
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling