8DQO

Crystal structure of Arabidopsis thaliana COSY


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4G0B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP298.1550 mM calcium acetate, 0.1 M sodium cacodylate pH 6.5, 20% glycerol
Crystal Properties
Matthews coefficientSolvent content
2.2645.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.411α = 90
b = 57.903β = 90
c = 270.395γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2017-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.9791APS24-ID-C

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
11.948.7298.65113.421.171357
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.96889.6411.1

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 REPLACEMENTTHROUGHOUT4G0B1.948.7667704365398.510.19160.18960.23017RANDOM32.958
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]
-0.74-0.521.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.175
r_dihedral_angle_4_deg17.835
r_dihedral_angle_3_deg14.345
r_dihedral_angle_1_deg6.645
r_long_range_B_refined4.892
r_long_range_B_other4.892
r_scangle_other1.742
r_mcangle_it1.5
r_mcangle_other1.5
r_angle_refined_deg1.326
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.175
r_dihedral_angle_4_deg17.835
r_dihedral_angle_3_deg14.345
r_dihedral_angle_1_deg6.645
r_long_range_B_refined4.892
r_long_range_B_other4.892
r_scangle_other1.742
r_mcangle_it1.5
r_mcangle_other1.5
r_angle_refined_deg1.326
r_scbond_it1.091
r_scbond_other1.088
r_angle_other_deg0.951
r_mcbond_it0.884
r_mcbond_other0.884
r_chiral_restr0.066
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.004
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 Atoms6806
Nucleic Acid Atoms
Solvent Atoms351
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing