6L32

Crystal structure of potassium induced heme modification in yak lactoperoxidase at 2.30 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
2.4950.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.7α = 90
b = 84.71β = 90
c = 98.75γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHmirror2019-09-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONRRCAT INDUS-2 BEAMLINE PX-BL210.97947RRCAT INDUS-2PX-BL21

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
12.358.1141000.20.985.96.830425
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)
12.32.3999.90.850.881.96.5

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-VALUE3BXI2.358.113036766399.9470.1910.19030.244227.013
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]
-1.087-1.052.137
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.892
r_dihedral_angle_3_deg19.183
r_dihedral_angle_4_deg14.384
r_lrange_it8.601
r_lrange_other8.576
r_dihedral_angle_1_deg7.694
r_mcangle_other4.307
r_mcangle_it4.305
r_scangle_it4.019
r_scangle_other4.019
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.892
r_dihedral_angle_3_deg19.183
r_dihedral_angle_4_deg14.384
r_lrange_it8.601
r_lrange_other8.576
r_dihedral_angle_1_deg7.694
r_mcangle_other4.307
r_mcangle_it4.305
r_scangle_it4.019
r_scangle_other4.019
r_mcbond_it2.522
r_mcbond_other2.505
r_scbond_other2.464
r_scbond_it2.463
r_angle_refined_deg1.651
r_angle_other_deg1.251
r_metal_ion_refined0.371
r_nbd_refined0.25
r_symmetry_xyhbond_nbd_refined0.243
r_nbd_other0.221
r_symmetry_nbd_other0.208
r_xyhbond_nbd_refined0.194
r_symmetry_nbd_refined0.174
r_nbtor_refined0.168
r_symmetry_xyhbond_nbd_other0.138
r_symmetry_metal_ion_refined0.086
r_symmetry_nbtor_other0.082
r_chiral_restr0.078
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_gen_planes_other0.005
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4784
Nucleic Acid Atoms
Solvent Atoms329
Heterogen Atoms117

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing