3OJT

Structure of native Fe-containing Homoprotocatechuate 2,3-Dioxygenase at 1.70 Ang resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IG9PDB entry 2IG9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529313% PEG6000, 0.125 M calcium chloride, 0.1 M Tris-HCl, Cryoprotectant 25% PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4249.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.747α = 90
b = 151.229β = 90
c = 96.385γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2010-05-15MSINGLE WAVELENGTH
21x-ray100CCDADSC QUANTUM 315r2010-03-21M
31x-ray100CCDADSC QUANTUM 315r2010-03-21M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9999SLSX10SA
2SYNCHROTRONSOLEIL BEAMLINE PROXIMA 11.7394SOLEILPROXIMA 1
3SYNCHROTRONSOLEIL BEAMLINE PROXIMA 11.7428SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
1,2,31.789.4398.30.0640.1048.63.4177378174363318.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.71.7998.60.4270.68223.325338

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 REPLACEMENTTHROUGHOUTPDB entry 2IG91.759.49165298861397.860.160990.159570.18796RANDOM20.596
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]
0.02-0.040.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.953
r_dihedral_angle_4_deg17.982
r_dihedral_angle_3_deg12.739
r_dihedral_angle_1_deg6.935
r_scangle_it3.585
r_scbond_it2.275
r_angle_refined_deg1.461
r_mcangle_it1.343
r_angle_other_deg0.914
r_mcbond_it0.772
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.953
r_dihedral_angle_4_deg17.982
r_dihedral_angle_3_deg12.739
r_dihedral_angle_1_deg6.935
r_scangle_it3.585
r_scbond_it2.275
r_angle_refined_deg1.461
r_mcangle_it1.343
r_angle_other_deg0.914
r_mcbond_it0.772
r_mcbond_other0.259
r_chiral_restr0.098
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11532
Nucleic Acid Atoms
Solvent Atoms1254
Heterogen Atoms130

Software

Software
Software NamePurpose
todata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling