4Z6V

Structure of H200Q variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-nitrocatechol at 1.37 Ang resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629314% PEG6000, 0.1M calcium chloride, 0.1M Tris-HCL
Crystal Properties
Matthews coefficientSolvent content
2.3948.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.18α = 90
b = 150.635β = 90
c = 96.103γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102008-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.9334ESRFID14-1

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
11.3745.69197.90.0640.0730.03514.24.1325847325847
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)
11.371.4495.90.7860.7860.43214.146253

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 REPLACEMENTTHROUGHOUT3OJT1.3740.353095391624997.690.12060.11870.1567RANDOM16.321
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]
-0.03-0.10.14
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free32.275
r_sphericity_bonded10.129
r_rigid_bond_restr1.975
r_mcangle_it1.806
r_mcbond_it1.519
r_mcbond_other1.517
r_angle_refined_deg1.357
r_angle_other_deg0.803
r_chiral_restr0.087
r_bond_refined_d0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free32.275
r_sphericity_bonded10.129
r_rigid_bond_restr1.975
r_mcangle_it1.806
r_mcbond_it1.519
r_mcbond_other1.517
r_angle_refined_deg1.357
r_angle_other_deg0.803
r_chiral_restr0.087
r_bond_refined_d0.009
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 Atoms11519
Nucleic Acid Atoms
Solvent Atoms1955
Heterogen Atoms114

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing