2PT3

Crystal structure of bovine lactoperoxidase at 2.34 A resolution reveals multiple anion binding sites


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.8298Tris-HCl, Phosphate, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3447.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.91α = 90
b = 80.051β = 103.23
c = 75.675γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200IMAGE PLATEMAR scanner 345 mm plateMirror2006-10-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X13EMBL/DESY, HAMBURGX13

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
12.3474.798.50.06426.52655324867
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.342.3899.8

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2NQX2.3419.38265532486782296.750.23190.231380.24682RANDOM61.388
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]
1.154.46-5.055.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg21.481
r_scangle_it3.863
r_dihedral_angle_1_deg3.693
r_scbond_it3.175
r_angle_refined_deg2.075
r_mcangle_it1.651
r_mcbond_it0.931
r_symmetry_vdw_refined0.349
r_nbd_refined0.283
r_metal_ion_refined0.218
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg21.481
r_scangle_it3.863
r_dihedral_angle_1_deg3.693
r_scbond_it3.175
r_angle_refined_deg2.075
r_mcangle_it1.651
r_mcbond_it0.931
r_symmetry_vdw_refined0.349
r_nbd_refined0.283
r_metal_ion_refined0.218
r_symmetry_hbond_refined0.211
r_xyhbond_nbd_refined0.209
r_chiral_restr0.129
r_bond_refined_d0.018
r_gen_planes_refined0.008
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 Atoms4774
Nucleic Acid Atoms
Solvent Atoms249
Heterogen Atoms258

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing