2O86

Crystal structure of a ternary complex of buffalo lactoperoxidase with nitrate and iodide at 2.8 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IPS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7298Tris-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4650.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.535α = 90
b = 80.833β = 102.96
c = 77.655γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATEMAR scanner 345 mm plateMirror2006-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU300

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.82097.81603414923
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.998.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2IPS2.820160341492379196.520.210.20910.208620.21777RANDOM39.53
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]
-0.65-0.52-1.411.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg22.152
r_dihedral_angle_1_deg5.65
r_scangle_it3.713
r_scbond_it2.201
r_angle_refined_deg2.089
r_mcangle_it1.71
r_mcbond_it0.916
r_symmetry_vdw_refined0.433
r_nbd_refined0.276
r_xyhbond_nbd_refined0.193
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg22.152
r_dihedral_angle_1_deg5.65
r_scangle_it3.713
r_scbond_it2.201
r_angle_refined_deg2.089
r_mcangle_it1.71
r_mcbond_it0.916
r_symmetry_vdw_refined0.433
r_nbd_refined0.276
r_xyhbond_nbd_refined0.193
r_chiral_restr0.136
r_symmetry_hbond_refined0.123
r_metal_ion_refined0.061
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4766
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms217

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing