3C6N | pdb_00003c6n

Small molecule agonists and antagonists of F-box protein-substrate interactions in auxin perception and signaling


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1P1M 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1627712-14% PEG 40,000 1mM BTP pH 6.0, 200mM NaCl, EVAPORATION, temperature 277K, pH 6.00
Crystal Properties
Matthews coefficientSolvent content
2.9558.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.51α = 90
b = 80.661β = 104.95
c = 125.071γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-07-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.2ALS5.0.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.650750.010422.86.2265412
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.675

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1P1M2.649.5225384126541144091.80.190.1850.20.2810.28RANDOM39.66
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]
0.44-0.011.65-2.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.898
r_dihedral_angle_3_deg22.056
r_dihedral_angle_4_deg19.252
r_dihedral_angle_1_deg9.937
r_scangle_it6.214
r_scbond_it4.115
r_angle_refined_deg3.422
r_mcangle_it2.495
r_mcbond_it1.506
r_nbtor_refined0.349
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.898
r_dihedral_angle_3_deg22.056
r_dihedral_angle_4_deg19.252
r_dihedral_angle_1_deg9.937
r_scangle_it6.214
r_scbond_it4.115
r_angle_refined_deg3.422
r_mcangle_it2.495
r_mcbond_it1.506
r_nbtor_refined0.349
r_nbd_refined0.307
r_symmetry_vdw_refined0.279
r_symmetry_hbond_refined0.244
r_chiral_restr0.233
r_xyhbond_nbd_refined0.221
r_bond_refined_d0.035
r_gen_planes_refined0.011
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 AtomsNumber
Protein Atoms4932
Nucleic Acid Atoms
Solvent Atoms177
Heterogen Atoms63

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing