3GCJ

Mode of ligand binding and assignment of subsites in mammalian peroxidases: crystal structure of lactoperoxidase complexes with acetyl salycylic acid, salicylhydroxamic acid and benzylhydroxamic acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.82980.2M ammonium Iodide, 20% PEG3350, pH6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4650.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.618α = 90
b = 80.553β = 102.55
c = 77.803γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray291IMAGE PLATEMAR scanner 345 mm platemirror2008-10-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54312

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
12.3419.4798.5278992743840.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.342.495.2

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 3BXI2.3419.47278992743880798.40.2040.2040.212RANDOM37.5
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]
-0.55-0.7-5.966.51
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.2
c_mcangle_it2.56
c_scangle_it1.94
c_angle_deg1.7
c_mcbond_it1.51
c_improper_angle_d1.23
c_scbond_it1.08
c_bond_d0.009
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.2
c_mcangle_it2.56
c_scangle_it1.94
c_angle_deg1.7
c_mcbond_it1.51
c_improper_angle_d1.23
c_scbond_it1.08
c_bond_d0.009
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 Atoms4775
Nucleic Acid Atoms
Solvent Atoms351
Heterogen Atoms200

Software

Software
Software NamePurpose
MAR345dtbdata collection
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling