3ERH

First structural evidence of substrate specificity in mammalian peroxidases: Crystal structures of substrate complexes with lactoperoxidases from two different species


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2R5LPDB ENTRY 2R5L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629810mM Phosphate buffre, 2mM CaCl2, 20% PEG3350, 0.2M Ammonium Iodide, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4449.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.207α = 90
b = 80.541β = 102.64
c = 77.877γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray291IMAGE PLATEMAR scanner 345 mm plateMirror2008-09-24MSINGLE 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
12.419.4698.6267962535548
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.599.9

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 2R5L2.419.46267962535549698.70.180.180.195RANDOM38.9
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]
-2.41-0.81-4.016.43
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.9
c_scangle_it4.89
c_scbond_it3.49
c_mcangle_it2.79
c_mcbond_it1.72
c_angle_deg1.7
c_improper_angle_d1.14
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.9
c_scangle_it4.89
c_scbond_it3.49
c_mcangle_it2.79
c_mcbond_it1.72
c_angle_deg1.7
c_improper_angle_d1.14
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4778
Nucleic Acid Atoms
Solvent Atoms398
Heterogen Atoms202

Software

Software
Software NamePurpose
MAR345dtbdata collection
AMoREphasing
CNSrefinement
AUTOMARdata reduction
SCALEPACKdata scaling