4Z6N

Structure of H200N variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum 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 acetate, 0.1M MOPS
Crystal Properties
Matthews coefficientSolvent content
2.3948.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.179α = 90
b = 150.663β = 90
c = 96.067γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-04-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.9801SOLEILPROXIMA 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
11.5248.0399.60.0650.0740.03513.44.4243620243620
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)
11.521.698.40.7510.7510.41214.234831

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 REPLACEMENTTHROUGHOUT3OJT1.5245.762314291211499.480.120.11750.1673RANDOM21.07
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]
-0.02-0.220.24
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free28.477
r_sphericity_bonded10.832
r_rigid_bond_restr3.656
r_mcangle_it2.733
r_mcbond_it2.501
r_mcbond_other2.493
r_angle_refined_deg1.516
r_angle_other_deg0.851
r_chiral_restr0.101
r_bond_refined_d0.013
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free28.477
r_sphericity_bonded10.832
r_rigid_bond_restr3.656
r_mcangle_it2.733
r_mcbond_it2.501
r_mcbond_other2.493
r_angle_refined_deg1.516
r_angle_other_deg0.851
r_chiral_restr0.101
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11536
Nucleic Acid Atoms
Solvent Atoms1696
Heterogen Atoms104

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing