2Z5Z

Crystal structure of the complex of buffalo Lactoperoxidase with fluoride ion at 3.5A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2O86PDB entry 2O86

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.2290TRIS-HCL, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.4449.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.127α = 90
b = 80.739β = 102.94
c = 77.699γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray290IMAGE PLATEMARRESEARCHMirror2007-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
13.575.8183.60.1293.93.1664164.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.53.6287.70.1841.93.16641

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 REPLACEMENTTHROUGHOUTPDB entry 2O863.575.81664132483.190.221820.221170.23484RANDOM27.023
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]
-0.71-0.93-4.64.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.636
r_dihedral_angle_3_deg18.978
r_dihedral_angle_4_deg15.72
r_dihedral_angle_1_deg2.376
r_angle_refined_deg1.991
r_symmetry_hbond_refined0.331
r_nbtor_refined0.327
r_symmetry_vdw_refined0.286
r_nbd_refined0.247
r_xyhbond_nbd_refined0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.636
r_dihedral_angle_3_deg18.978
r_dihedral_angle_4_deg15.72
r_dihedral_angle_1_deg2.376
r_angle_refined_deg1.991
r_symmetry_hbond_refined0.331
r_nbtor_refined0.327
r_symmetry_vdw_refined0.286
r_nbd_refined0.247
r_xyhbond_nbd_refined0.18
r_chiral_restr0.131
r_metal_ion_refined0.09
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_mcbond_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4770
Nucleic Acid Atoms
Solvent Atoms26
Heterogen Atoms194

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
AUTOMARdata reduction
SCALEPACKdata scaling
AMoREphasing