3R4X

Crystal structure of bovine lactoperoxidase complexed with pyrazine-2-carboxamide at 2 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.8298Ammonium Iodide, PEG3350, pH6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K , pH 6.8 , temperature 298 K
Crystal Properties
Matthew coefficientSolvent content
2.3848.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.924α = 90
b = 79.717β = 102.22
c = 77.005γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHMIRROR2010-10-21MSINGLE 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
1275.26960.087303947423.7
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)
12.012.0690.50.423.8

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 3GC12.0175.263947439474210497.80.2130.210.256RANDOM36.34
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]
-1.83-0.12-2.574.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.286
r_dihedral_angle_4_deg16.939
r_dihedral_angle_3_deg13.662
r_dihedral_angle_1_deg2.511
r_angle_refined_deg2.185
r_mcangle_it1.997
r_scangle_it1.89
r_scbond_it1.513
r_mcbond_it1.177
r_chiral_restr0.184
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.286
r_dihedral_angle_4_deg16.939
r_dihedral_angle_3_deg13.662
r_dihedral_angle_1_deg2.511
r_angle_refined_deg2.185
r_mcangle_it1.997
r_scangle_it1.89
r_scbond_it1.513
r_mcbond_it1.177
r_chiral_restr0.184
r_bond_refined_d0.021
r_gen_planes_refined0.014
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_bond_other_d
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_sphericity_bonded
r_mcbond_other
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4774
Nucleic Acid Atoms
Solvent Atoms499
Heterogen Atoms195

Software

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