4LDY

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.75 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 coefficientSolvent content
2.6954.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.1α = 90
b = 84.24β = 114.76
c = 78.96γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2012-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.9795ALBAXALOC

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
12.371.799.90.1025.93.138764-341.1
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)
12.32.421000.631.83.25641

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB ENTRY 4LDV2.363.9136804194399.870.212630.210150.2588RANDOM60.556
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]
-0.831.33-0.580.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.148
r_dihedral_angle_4_deg17.695
r_dihedral_angle_3_deg17.289
r_dihedral_angle_1_deg7.532
r_long_range_B_refined7.115
r_long_range_B_other7.104
r_scangle_other4.215
r_mcangle_it3.83
r_mcangle_other3.83
r_scbond_it2.604
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.148
r_dihedral_angle_4_deg17.695
r_dihedral_angle_3_deg17.289
r_dihedral_angle_1_deg7.532
r_long_range_B_refined7.115
r_long_range_B_other7.104
r_scangle_other4.215
r_mcangle_it3.83
r_mcangle_other3.83
r_scbond_it2.604
r_scbond_other2.604
r_mcbond_it2.368
r_mcbond_other2.368
r_angle_refined_deg1.641
r_angle_other_deg0.799
r_chiral_restr0.09
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms5239
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling