3BXI

Structure of the complex of bovine lactoperoxidase with its catalyzed product hypothiocyanate ion at 2.3A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1CXPPDB ENTRY 1CXP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2298NaNO3, PEG3350, pH6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4650.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.63α = 90
b = 80.667β = 102.6
c = 77.68γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray292IMAGE PLATEMAR scanner 345 mm plateMirror2007-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54132

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
12.375.8199.32935627641
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3499.4

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1CXP2.324.462935627641147799.20.170960.168350.21803RANDOM29.265
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]
0.26-0.81-0.630.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.75
r_dihedral_angle_1_deg3.828
r_scangle_it3.224
r_scbond_it1.884
r_angle_refined_deg1.73
r_mcangle_it1.472
r_mcbond_it0.77
r_symmetry_vdw_refined0.276
r_nbd_refined0.247
r_symmetry_hbond_refined0.204
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.75
r_dihedral_angle_1_deg3.828
r_scangle_it3.224
r_scbond_it1.884
r_angle_refined_deg1.73
r_mcangle_it1.472
r_mcbond_it0.77
r_symmetry_vdw_refined0.276
r_nbd_refined0.247
r_symmetry_hbond_refined0.204
r_xyhbond_nbd_refined0.155
r_chiral_restr0.104
r_metal_ion_refined0.076
r_bond_refined_d0.009
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 Atoms413
Heterogen Atoms205

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing