8Y9X

Crystal structure of the complex of lactoperoxidase with four inorganic substrates, SCN, I, Br and Cl


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8K5M 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.22980.2 M Ammonium iodide, 20%(w/v) PEG 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298 K
Crystal Properties
Matthews coefficientSolvent content
2.2545.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.35α = 90
b = 80.332β = 103.94
c = 73.391γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDMARMOSAIC 325 mm CCD2010-10-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97ESRFBM14

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
11.9943.52196.70.08229.86.239294
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)
11.992.05770.314.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE8K5M243.52139294197196.4960.1530.15060.195129.645
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]
-0.035-0.010.055-0.013
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.321
r_dihedral_angle_3_deg13.041
r_lrange_it9.892
r_lrange_other9.869
r_dihedral_angle_1_deg6.873
r_dihedral_angle_2_deg6.812
r_scangle_it5.743
r_scangle_other5.743
r_mcangle_other5.335
r_mcangle_it5.334
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.321
r_dihedral_angle_3_deg13.041
r_lrange_it9.892
r_lrange_other9.869
r_dihedral_angle_1_deg6.873
r_dihedral_angle_2_deg6.812
r_scangle_it5.743
r_scangle_other5.743
r_mcangle_other5.335
r_mcangle_it5.334
r_scbond_it3.463
r_scbond_other3.463
r_mcbond_it3.283
r_mcbond_other3.273
r_angle_refined_deg1.684
r_angle_other_deg0.783
r_symmetry_nbd_refined0.347
r_nbd_other0.313
r_nbd_refined0.227
r_symmetry_nbd_other0.213
r_symmetry_xyhbond_nbd_refined0.207
r_nbtor_refined0.183
r_xyhbond_nbd_refined0.181
r_symmetry_nbtor_other0.111
r_chiral_restr0.085
r_symmetry_xyhbond_nbd_other0.047
r_bond_other_d0.013
r_gen_planes_other0.011
r_gen_planes_refined0.01
r_bond_refined_d0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4742
Nucleic Acid Atoms
Solvent Atoms407
Heterogen Atoms205

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building