4LDU

Crystal structure of the DNA binding domain of Arabidopsis thaliana auxin response factor 5


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293100 nL 13 mg/mL ARF5DBD +100 nl crystallization buffer (20 mM TRIS 7.5, 12.5% PEG MME 2000), VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5351.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.613α = 90
b = 91.502β = 114.28
c = 77.182γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102010-05-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.93340ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.154599.80.063112.823983-330.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.271000.432.92.83492

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.1538.3822772121199.690.197710.194750.25206RANDOM26.435
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]
-2.43-0.46-2.393.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.58
r_dihedral_angle_4_deg24.08
r_dihedral_angle_3_deg17.921
r_dihedral_angle_1_deg7
r_long_range_B_refined6.686
r_mcangle_it2.737
r_scbond_it2.047
r_mcbond_it1.748
r_angle_refined_deg1.626
r_chiral_restr0.108
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.58
r_dihedral_angle_4_deg24.08
r_dihedral_angle_3_deg17.921
r_dihedral_angle_1_deg7
r_long_range_B_refined6.686
r_mcangle_it2.737
r_scbond_it2.047
r_mcbond_it1.748
r_angle_refined_deg1.626
r_chiral_restr0.108
r_bond_refined_d0.013
r_gen_planes_refined0.008
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 AtomsNumber
Protein Atoms2651
Nucleic Acid Atoms
Solvent Atoms189
Heterogen Atoms2

Software

Software
Software NamePurpose
MxCuBEdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling