7D52

Crystal structure of yak lactoperoxidase with a disordered propionic group of heme moiety at 2.20 A resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.82980.2M potassium fluoride, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.5151.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.98α = 90
b = 85.08β = 90
c = 98.93γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6Mmirror2019-09-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C1.0ELETTRA11.2C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)CC (Half)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
12.2851000.20.99310.21235006
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2799.90.990.9673.111

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-VALUE3BXI2.262.27434747180699.4160.1930.19020.249828.912
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]
0.031-0.0410.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.997
r_dihedral_angle_4_deg16.894
r_dihedral_angle_3_deg15.309
r_lrange_it8.505
r_dihedral_angle_1_deg7.161
r_scangle_it4.385
r_mcangle_it3.99
r_scbond_it2.83
r_mcbond_it2.412
r_angle_refined_deg1.522
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.997
r_dihedral_angle_4_deg16.894
r_dihedral_angle_3_deg15.309
r_lrange_it8.505
r_dihedral_angle_1_deg7.161
r_scangle_it4.385
r_mcangle_it3.99
r_scbond_it2.83
r_mcbond_it2.412
r_angle_refined_deg1.522
r_metal_ion_refined0.321
r_nbtor_refined0.314
r_symmetry_xyhbond_nbd_refined0.266
r_nbd_refined0.224
r_symmetry_nbd_refined0.201
r_xyhbond_nbd_refined0.186
r_chiral_restr0.114
r_bond_refined_d0.007
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4770
Nucleic Acid Atoms
Solvent Atoms450
Heterogen Atoms118

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing