5BWH

Structure of H200C variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with HPCA at 1.46 Ang resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729313-15% PEG6K, 0.1M calcium chloride, 0.1M MOPS
Crystal Properties
Matthews coefficientSolvent content
2.4148.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.414α = 90
b = 151.027β = 90
c = 96.468γ = 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 I030.9763DiamondI03

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
11.4629.796.90.0590.0680.03412.33.8269165269165
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)
11.461.54940.710.710.40923.837792

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 REPLACEMENTTHROUGHOUT3OJT1.4629.662557301339196.690.12360.12170.1605RANDOM20.44
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]
0.16-0.1-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free25.746
r_sphericity_bonded9.969
r_rigid_bond_restr2.408
r_mcangle_it2.17
r_mcbond_it1.904
r_mcbond_other1.898
r_angle_refined_deg1.301
r_angle_other_deg0.789
r_chiral_restr0.087
r_bond_refined_d0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free25.746
r_sphericity_bonded9.969
r_rigid_bond_restr2.408
r_mcangle_it2.17
r_mcbond_it1.904
r_mcbond_other1.898
r_angle_refined_deg1.301
r_angle_other_deg0.789
r_chiral_restr0.087
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 Atoms11555
Nucleic Acid Atoms
Solvent Atoms1506
Heterogen Atoms126

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing