2OJV

Crystal structure of a ternary complex of goat lactoperoxidase with cyanide and iodide ions at 2.4 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GJ1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.2298100mM Tris-Hcl, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4349.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.197α = 90
b = 80.811β = 102.96
c = 77.047γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray292IMAGE PLATEMAR scanner 345 mm platemirror2006-10-10MSINGLE 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
12.474.5497.92496223672
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4490.1

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2GJ12.474.542496223672127497.790.1920.1820.178390.22786RANDOM27.265
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]
0.46-0.82-1.380.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.504
r_dihedral_angle_1_deg4.448
r_scangle_it3.942
r_scbond_it2.381
r_angle_refined_deg1.98
r_mcangle_it1.681
r_mcbond_it0.89
r_symmetry_hbond_refined0.313
r_nbd_refined0.26
r_symmetry_vdw_refined0.212
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.504
r_dihedral_angle_1_deg4.448
r_scangle_it3.942
r_scbond_it2.381
r_angle_refined_deg1.98
r_mcangle_it1.681
r_mcbond_it0.89
r_symmetry_hbond_refined0.313
r_nbd_refined0.26
r_symmetry_vdw_refined0.212
r_xyhbond_nbd_refined0.189
r_metal_ion_refined0.138
r_chiral_restr0.12
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4753
Nucleic Acid Atoms
Solvent Atoms406
Heterogen Atoms203

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing