5ELW

A. thaliana IGPD2 in complex with the triazole-phosphonate inhibitor, (R)-C348, to 1.36A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52900.1M Tris-HCl pH8.5 and 20% PEG 300
Crystal Properties
Matthews coefficientSolvent content
2.6653.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.58α = 90
b = 112.58β = 90
c = 112.58γ = 90
Symmetry
Space GroupP 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-10-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.98020DiamondI04

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
11.3645.96990.06823.89.15215652156
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)
11.361.489.10.662.87.5

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 REPLACEMENTTHROUGHOUT5EKW1.445.9647188122599.80.11720.116660.1312RANDOM11.722
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.662
r_sphericity_free20.309
r_dihedral_angle_4_deg18.546
r_dihedral_angle_3_deg10.885
r_sphericity_bonded10.108
r_rigid_bond_restr8.409
r_dihedral_angle_1_deg6.604
r_scbond_other2.9
r_scbond_it2.898
r_long_range_B_refined2.434
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.662
r_sphericity_free20.309
r_dihedral_angle_4_deg18.546
r_dihedral_angle_3_deg10.885
r_sphericity_bonded10.108
r_rigid_bond_restr8.409
r_dihedral_angle_1_deg6.604
r_scbond_other2.9
r_scbond_it2.898
r_long_range_B_refined2.434
r_long_range_B_other2.433
r_scangle_other2.37
r_angle_other_deg1.825
r_angle_refined_deg1.59
r_mcangle_other1.111
r_mcangle_it1.108
r_mcbond_it0.942
r_mcbond_other0.931
r_chiral_restr0.096
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.004
r_gen_planes_other0.004
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 Atoms1533
Nucleic Acid Atoms
Solvent Atoms204
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing