4DGQ

Crystal structure of Non-heme chloroperoxidase from Burkholderia cenocepacia


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZOIPDB entry 1zoi

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP290Internal tracking number 228044H10. Wizard III/IV screen condition H10: 30% 2-propanol, 30% PEG3350, 0.1 M Tris, pH 8.5. BuceA00095hA1 PS01264 at 21.88mg/ml in a stabilizing buffer of 25 mM HEPES, pH 7.0, 500 mM NaCl, 2 mM DTT, 0.025% sodium azide, 5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.7655.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.77α = 90
b = 111.85β = 111.65
c = 80.21γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2012-01-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.541780

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.855099.70.09920.7711.184726-319.591
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.998.10.5042.73.2

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 DIFFRACTIONMRTHROUGHOUTPDB entry 1zoi1.8539.5984695422399.810.1360.1350.163RANDOM13.905
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]
0.020.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.278
r_dihedral_angle_4_deg22.121
r_dihedral_angle_3_deg12.404
r_dihedral_angle_1_deg5.571
r_angle_refined_deg1.595
r_angle_other_deg0.97
r_chiral_restr0.106
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.278
r_dihedral_angle_4_deg22.121
r_dihedral_angle_3_deg12.404
r_dihedral_angle_1_deg5.571
r_angle_refined_deg1.595
r_angle_other_deg0.97
r_chiral_restr0.106
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6394
Nucleic Acid Atoms
Solvent Atoms858
Heterogen Atoms12

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing