5B72

Crystal structure of bovine lactoperoxidase with a broken covalent bond between Glu258 and heme moiety at 1.98 A resolution.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4S0Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.82980.2M AMMONIUM IODIDE, 20% PEG3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, 298K.
Crystal Properties
Matthews coefficientSolvent content
2.2344.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.847α = 90
b = 80.192β = 105.41
c = 75.086γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray291CCDMARRESEARCHMIRROR2015-09-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.98ESRFBM14

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
11.9872.3996.70.1511.53.24163127.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.982.0169.10.661.1

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 REPLACEMENTTHROUGHOUT4S0Y1.9872.3939591165595.840.189930.188040.23508RANDOM39.576
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]
0.73-1.3-1.881.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.686
r_dihedral_angle_3_deg16.325
r_dihedral_angle_4_deg15.408
r_long_range_B_refined10.908
r_long_range_B_other10.885
r_dihedral_angle_1_deg7.501
r_scangle_other6.498
r_mcangle_it5.651
r_mcangle_other5.649
r_scbond_it4.201
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.686
r_dihedral_angle_3_deg16.325
r_dihedral_angle_4_deg15.408
r_long_range_B_refined10.908
r_long_range_B_other10.885
r_dihedral_angle_1_deg7.501
r_scangle_other6.498
r_mcangle_it5.651
r_mcangle_other5.649
r_scbond_it4.201
r_scbond_other4.2
r_mcbond_it3.571
r_mcbond_other3.569
r_angle_refined_deg2.062
r_angle_other_deg1.182
r_chiral_restr0.129
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_gen_planes_other0.005
r_bond_other_d0.004
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 Atoms4763
Nucleic Acid Atoms
Solvent Atoms262
Heterogen Atoms152

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing