2IGA

Structure of Homoprotocatechuate 2,3-Dioxygenase from B. fuscum in complex with reactive intermediates formed via in crystallo reaction with 4-nitrocatechol at low oxygen concentrations.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1F1XPDB ENTRY 1F1X

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.529218% PEG8000, 0.2 M calcium acetate, 0.1 M sodium cacodylate. Prior to freezing in liquid nitrogen, crystals were sequentially transferred into mother liquor solutions containing 5, 10, 15, and then 20% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K, pH 6.50
Crystal Properties
Matthews coefficientSolvent content
2.2545.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.678α = 90
b = 153.022β = 90
c = 96.389γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDNOIR-12006-05-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.2ALS4.2.2

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
11.9552.787.80.0955.42.08105058
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)
11.952.0291.60.3791.92.16

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 1F1X1.9552.7104994104994527787.80.1850.24532.59
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.727
r_dihedral_angle_4_deg18.432
r_dihedral_angle_3_deg14.294
r_dihedral_angle_1_deg7.34
r_scangle_it3.467
r_scbond_it2.55
r_angle_refined_deg1.671
r_mcangle_it1.36
r_mcbond_it1.112
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.727
r_dihedral_angle_4_deg18.432
r_dihedral_angle_3_deg14.294
r_dihedral_angle_1_deg7.34
r_scangle_it3.467
r_scbond_it2.55
r_angle_refined_deg1.671
r_mcangle_it1.36
r_mcbond_it1.112
r_nbtor_refined0.308
r_nbd_refined0.21
r_symmetry_metal_ion_refined0.195
r_symmetry_vdw_refined0.177
r_xyhbond_nbd_refined0.162
r_symmetry_hbond_refined0.144
r_chiral_restr0.122
r_metal_ion_refined0.096
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11600
Nucleic Acid Atoms
Solvent Atoms1042
Heterogen Atoms139

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
CCP4phasing