1H1I | pdb_00001h1i

CRYSTAL STRUCTURE OF QUERCETIN 2,3-DIOXYGENASE ANAEROBICALLY COMPLEXED WITH THE SUBSTRATE QUERCETN


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.2HANGING DROP, 21-23% PEG 8000, 200 MM AMMONIUM SULFATE, 100 MM CITRATE BUFFER, PH 5.2
Crystal Properties
Matthews coefficientSolvent content
2.3246.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.298α = 90
b = 55.745β = 98.39
c = 124.163γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.755099.50.06228.24.3148198
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)
11.751.7669.40.253.62.1

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 DIFFRACTIONOTHERTHROUGHOUT1.7549.39141342747399.50.150.1480.18950.1830.2144RANDOM14.52
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]
0.50.341.35-1.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.406
r_scangle_it3.696
r_scbond_it2.397
r_angle_refined_deg1.564
r_mcangle_it1.392
r_mcbond_it0.814
r_nbd_refined0.204
r_symmetry_vdw_refined0.191
r_symmetry_hbond_refined0.137
r_xyhbond_nbd_refined0.122
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.406
r_scangle_it3.696
r_scbond_it2.397
r_angle_refined_deg1.564
r_mcangle_it1.392
r_mcbond_it0.814
r_nbd_refined0.204
r_symmetry_vdw_refined0.191
r_symmetry_hbond_refined0.137
r_xyhbond_nbd_refined0.122
r_chiral_restr0.117
r_bond_refined_d0.016
r_metal_ion_refined0.009
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10580
Nucleic Acid Atoms
Solvent Atoms1539
Heterogen Atoms404

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling