3OJJ

Structure of Co-substituted Homoprotocatechuate 2,3-Dioxygenase from B.fuscum at 1.72 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, 0.1 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
2.4349.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.539α = 90
b = 152.075β = 90
c = 96.491γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-04-14MSINGLE WAVELENGTH
21x-ray100CCDADSC QUANTUM 315r2010-03-21MSINGLE WAVELENGTH
31x-ray100CCDADSC QUANTUM 315r2010-03-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03
2SYNCHROTRONSOLEIL BEAMLINE PROXIMA 11.6050SOLEILPROXIMA 1
3SYNCHROTRONSOLEIL BEAMLINE PROXIMA 11.6077SOLEILPROXIMA 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
1,2,31.7229.8698.90.0630.10393.5172043170151316.7
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)
1.721.8198.70.4371.93.524631

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 2IG91.7229.62161661844298.640.148140.146640.17639RANDOM18.684
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]
0.010.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.124
r_dihedral_angle_4_deg18.473
r_dihedral_angle_3_deg12.334
r_dihedral_angle_1_deg7.15
r_scangle_it3.06
r_scbond_it2
r_angle_refined_deg1.442
r_mcangle_it1.116
r_angle_other_deg0.915
r_mcbond_it0.664
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.124
r_dihedral_angle_4_deg18.473
r_dihedral_angle_3_deg12.334
r_dihedral_angle_1_deg7.15
r_scangle_it3.06
r_scbond_it2
r_angle_refined_deg1.442
r_mcangle_it1.116
r_angle_other_deg0.915
r_mcbond_it0.664
r_mcbond_other0.225
r_chiral_restr0.096
r_bond_refined_d0.014
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 Atoms11523
Nucleic Acid Atoms
Solvent Atoms1651
Heterogen Atoms130

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling