4LDY | pdb_00004ldy

Crystal structure of the DNA binding domain of the G245A mutant of arabidopsis thaliana auxin reponse factor 1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4LDV	PDB ENTRY 4LDV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	0.75 l of 13 mg/ml Arf1dbd-g245a +0.75 l crystallization buffer (100 mM bis-tris-propane pH 7.0, 0.7 M succinic acid), VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.1	α = 90
b = 84.24	β = 114.76
c = 78.96	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	PSI PILATUS 6M		2012-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.9795	ALBA	XALOC

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	2.3	71.7	99.9	0.102	5.9	3.1		38764		-3	41.1

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	2.3	2.42	100		0.63	1.8	3.2	5641

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	PDB ENTRY 4LDV	2.3	63.91	36804	1943	99.87	0.21263	0.21015	0.21	0.2588	0.26	RANDOM	60.556

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]
-0.83		1.33	-0.58		0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.148
r_dihedral_angle_4_deg	17.695
r_dihedral_angle_3_deg	17.289
r_dihedral_angle_1_deg	7.532
r_long_range_B_refined	7.115
r_long_range_B_other	7.104
r_scangle_other	4.215
r_mcangle_it	3.83
r_mcangle_other	3.83
r_scbond_it	2.604
r_scbond_other	2.604
r_mcbond_it	2.368
r_mcbond_other	2.368
r_angle_refined_deg	1.641
r_angle_other_deg	0.799
r_chiral_restr	0.09
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5239
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	2

Software

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