9IOY | pdb_00009ioy

Isophthalate dioxygenase in complex with isophthalate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293ammonium fluoride 0.2 M, PEG 3350 20%, 0.1 M MES pH 6.0
Crystal Properties
Matthews coefficientSolvent content
5.2976.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 146.956α = 90
b = 146.956β = 90
c = 146.956γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELRIGAKU HyPix-6000HE2022-07-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
13.325.2298.70.9659.93.715945
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)
13.33.570.9352.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT3.325.221534277299.590.176520.174560.18110.217640.2258RANDOM67.196
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_3_deg17.959
r_long_range_B_refined14.51
r_long_range_B_other14.509
r_scangle_other11.671
r_mcangle_it10.256
r_mcangle_other10.256
r_dihedral_angle_2_deg10.218
r_dihedral_angle_1_deg7.989
r_scbond_it7.519
r_scbond_other7.517
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.959
r_long_range_B_refined14.51
r_long_range_B_other14.509
r_scangle_other11.671
r_mcangle_it10.256
r_mcangle_other10.256
r_dihedral_angle_2_deg10.218
r_dihedral_angle_1_deg7.989
r_scbond_it7.519
r_scbond_other7.517
r_mcbond_it6.586
r_mcbond_other6.578
r_angle_refined_deg1.958
r_angle_other_deg0.647
r_chiral_restr0.085
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms3467
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing