5GH0

Crystal structure of the complex of bovine lactoperoxidase with mercaptoimidazole at 2.3 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BXI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.2280Tris hydrochloride, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Crystal Properties
Matthews coefficientSolvent content
2.3247

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-ray291IMAGE PLATEMARRESEARCHMIRROR2006-02-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

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
12.32099.40.081.54.229132
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3699.4

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 REPLACEMENTTHROUGHOUT3BXI2.3202818893299.20.14330.141570.19433RANDOM33.809
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]
0.42-0.76-0.390.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.065
r_dihedral_angle_3_deg16.874
r_dihedral_angle_4_deg15.803
r_long_range_B_refined11.369
r_long_range_B_other11.369
r_dihedral_angle_1_deg7.052
r_scangle_other6.258
r_mcangle_other6.177
r_mcangle_it6.175
r_scbond_it3.645
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.065
r_dihedral_angle_3_deg16.874
r_dihedral_angle_4_deg15.803
r_long_range_B_refined11.369
r_long_range_B_other11.369
r_dihedral_angle_1_deg7.052
r_scangle_other6.258
r_mcangle_other6.177
r_mcangle_it6.175
r_scbond_it3.645
r_scbond_other3.645
r_mcbond_it3.578
r_mcbond_other3.555
r_angle_refined_deg1.899
r_angle_other_deg1.151
r_chiral_restr0.123
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_gen_planes_other0.006
r_bond_other_d0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
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 Atoms290
Heterogen Atoms132

Software

Software
Software NamePurpose
REFMACrefinement
AUTOMARdata reduction
SCALEPACKdata scaling
MOLREPphasing