4Z6T

Structure of H200N variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-sulfonyl catechol at 1.50 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 acetate, 0.1M Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.3748.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.183α = 90
b = 149.939β = 90
c = 95.76γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2011-10-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9173DiamondI04-1

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
11.529.4998.60.090.10.04411.64.9248661248661
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)
11.51.5895.70.7960.7960.39114.934928

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 REPLACEMENTTHROUGHOUT3OJT1.529.492362081239498.410.11810.11580.1621RANDOM17.123
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]
0.07-0.180.11
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free30.805
r_sphericity_bonded9.12
r_rigid_bond_restr2.641
r_mcangle_it2.069
r_mcbond_it1.773
r_mcbond_other1.771
r_angle_refined_deg1.407
r_angle_other_deg0.82
r_chiral_restr0.093
r_bond_refined_d0.011
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free30.805
r_sphericity_bonded9.12
r_rigid_bond_restr2.641
r_mcangle_it2.069
r_mcbond_it1.773
r_mcbond_other1.771
r_angle_refined_deg1.407
r_angle_other_deg0.82
r_chiral_restr0.093
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11524
Nucleic Acid Atoms
Solvent Atoms1758
Heterogen Atoms142

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing