8DQR

Crystal structure of Arabidopsis thaliana COSY in complex with scopoletin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8DQO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP298.1550 mM calcium acetate, 0.1 M sodium cacodylate pH 6.5, 20% glycerol, 500 uM coenzyme-A, 5 mg/mL protein
Crystal Properties
Matthews coefficientSolvent content
2.5351.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.514α = 90
b = 88.886β = 90
c = 96.901γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.9791APS24-ID-E

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.2665.597.020.99912.69223643
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.262.34190.690.76220.76220.4250.892

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 REPLACEMENTTHROUGHOUT8DQO2.2665.522455118997.210.196360.191220.29135RANDOM52.561
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]
2.84-2.67-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.952
r_dihedral_angle_2_deg36.189
r_dihedral_angle_4_deg20.86
r_dihedral_angle_3_deg18.709
r_sphericity_bonded18.213
r_dihedral_angle_1_deg7.691
r_long_range_B_refined5.644
r_long_range_B_other5.629
r_mcangle_other4.81
r_mcangle_it4.806
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.952
r_dihedral_angle_2_deg36.189
r_dihedral_angle_4_deg20.86
r_dihedral_angle_3_deg18.709
r_sphericity_bonded18.213
r_dihedral_angle_1_deg7.691
r_long_range_B_refined5.644
r_long_range_B_other5.629
r_mcangle_other4.81
r_mcangle_it4.806
r_scangle_other4.744
r_scbond_it3.792
r_scbond_other3.79
r_mcbond_it3.612
r_mcbond_other3.594
r_rigid_bond_restr1.86
r_angle_refined_deg1.585
r_angle_other_deg0.907
r_chiral_restr0.076
r_bond_refined_d0.011
r_gen_planes_refined0.006
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3385
Nucleic Acid Atoms
Solvent Atoms143
Heterogen Atoms55

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing