4OEK

Crystal Structure of the Complex of goat Lactoperoxidase with Phenylethylamine at 2.47 A Resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3SXVPDB ENTRY 3SXV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.8298Sodium nitrate, PEG , pH 6.8 , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3146.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.166α = 90
b = 79.891β = 101.8
c = 75.284γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHMIRROR2013-11-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
12.4774.2189.20.08126.418577
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.472.5491.20.2994.9

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3SXV2.4773.6918577995880.2080.2040.281RANDOM44.161
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]
-1.03-2.22-1.922.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.677
r_dihedral_angle_4_deg18.634
r_dihedral_angle_3_deg16.103
r_dihedral_angle_1_deg6.323
r_angle_other_deg3.072
r_angle_refined_deg1.841
r_chiral_restr0.078
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_gen_planes_other0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.677
r_dihedral_angle_4_deg18.634
r_dihedral_angle_3_deg16.103
r_dihedral_angle_1_deg6.323
r_angle_other_deg3.072
r_angle_refined_deg1.841
r_chiral_restr0.078
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_gen_planes_other0.007
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4757
Nucleic Acid Atoms
Solvent Atoms250
Heterogen Atoms159

Software

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