5GLS

Structure of bovine Lactoperoxidase with a partially modified covalent bond with heme moiety


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.8298Ammonium Iodide, PEG, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.005α = 90
b = 79.834β = 102.3
c = 76.126γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRROR2014-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97ESRFBM14

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
11.93501000.0824.24.64754826.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.931.961002.24.4

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 REPLACEMENTTHROUGHOUT4S0Y1.935045122240699.960.194590.191810.24548RANDOM40.953
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]
-0.13-0.47-2.382.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.819
r_dihedral_angle_4_deg16.672
r_dihedral_angle_3_deg15.933
r_long_range_B_refined8.944
r_long_range_B_other8.944
r_dihedral_angle_1_deg7.966
r_mcangle_it6.091
r_mcangle_other6.085
r_scangle_other5.996
r_mcbond_it4.075
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.819
r_dihedral_angle_4_deg16.672
r_dihedral_angle_3_deg15.933
r_long_range_B_refined8.944
r_long_range_B_other8.944
r_dihedral_angle_1_deg7.966
r_mcangle_it6.091
r_mcangle_other6.085
r_scangle_other5.996
r_mcbond_it4.075
r_mcbond_other4.057
r_scbond_it3.945
r_scbond_other3.945
r_angle_refined_deg2.092
r_angle_other_deg1.158
r_chiral_restr0.129
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_gen_planes_other0.006
r_bond_other_d0.003
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 Atoms4771
Nucleic Acid Atoms
Solvent Atoms346
Heterogen Atoms149

Software

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