4Z6Z

Structure of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-sulfonyl catechol at 1.52 Ang resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OJT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729314% PEG6000, 0.1M calcium chloride, 0.1M MOPS
Crystal Properties
Matthews coefficientSolvent content
2.4148.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.399α = 90
b = 151.247β = 90
c = 96.158γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2012-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9762DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.5229.7297.50.0680.0770.034124.6239601239601
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.521.693.90.6750.6750.3591.14.333400

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 REPLACEMENTTHROUGHOUT3OJT1.5229.512276291192297.190.12260.12060.1609RANDOM20.167
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]
0.1-0.310.21
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free23.365
r_sphericity_bonded9.116
r_rigid_bond_restr2.73
r_mcangle_it2.162
r_mcbond_it1.938
r_mcbond_other1.938
r_angle_refined_deg1.289
r_angle_other_deg0.793
r_chiral_restr0.086
r_bond_refined_d0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free23.365
r_sphericity_bonded9.116
r_rigid_bond_restr2.73
r_mcangle_it2.162
r_mcbond_it1.938
r_mcbond_other1.938
r_angle_refined_deg1.289
r_angle_other_deg0.793
r_chiral_restr0.086
r_bond_refined_d0.009
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 Atoms1392
Heterogen Atoms167

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing