4Z6M

Structure of H200Q variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum at 1.35 Ang resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.429314% PEG6000, 0.1M calcium chloride, 0.1M MES
Crystal Properties
Matthews coefficientSolvent content
2.4249.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.485α = 90
b = 152.089β = 90
c = 96.188γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.000SLSX06DA

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
11.3548.09496.10.0940.1040.04511.35.2338753338753
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)
11.351.42930.7690.7690.3661547581

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 REPLACEMENTTHROUGHOUT3OJT1.3548.093217881691095.940.11350.11210.1397RANDOM12.958
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]
0.03-0.070.04
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free27.05
r_sphericity_bonded7.576
r_rigid_bond_restr1.98
r_angle_refined_deg1.369
r_mcangle_it1.209
r_mcbond_it0.969
r_mcbond_other0.967
r_angle_other_deg0.796
r_chiral_restr0.088
r_bond_refined_d0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free27.05
r_sphericity_bonded7.576
r_rigid_bond_restr1.98
r_angle_refined_deg1.369
r_mcangle_it1.209
r_mcbond_it0.969
r_mcbond_other0.967
r_angle_other_deg0.796
r_chiral_restr0.088
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 Atoms11600
Nucleic Acid Atoms
Solvent Atoms1968
Heterogen Atoms9

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing