7C75

Crystal structure of yak lactoperoxidase with partially coordinated Na ion in the distal heme cavity


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6L3Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.82980.2M Sodium Fluoride, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.4750.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.91α = 90
b = 84.83β = 90
c = 98.56γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2Mmirror2019-09-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C1.00ELETTRA11.2C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
12.764.399.30.20.090.977.19.918790
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.7797.61.050.340.832.89.3

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-VALUE6L3Z2.764.2951878989398.9310.1970.1930.267525.515
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]
0.0610.172-0.233
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.907
r_dihedral_angle_3_deg19.104
r_dihedral_angle_4_deg15.146
r_dihedral_angle_1_deg8.188
r_lrange_it8.134
r_lrange_other8.07
r_mcangle_other4.476
r_mcangle_it4.472
r_scangle_it3.675
r_scangle_other3.674
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.907
r_dihedral_angle_3_deg19.104
r_dihedral_angle_4_deg15.146
r_dihedral_angle_1_deg8.188
r_lrange_it8.134
r_lrange_other8.07
r_mcangle_other4.476
r_mcangle_it4.472
r_scangle_it3.675
r_scangle_other3.674
r_mcbond_it2.585
r_mcbond_other2.549
r_scbond_other2.098
r_scbond_it2.097
r_angle_refined_deg1.648
r_angle_other_deg1.192
r_symmetry_xyhbond_nbd_refined0.332
r_xyhbond_nbd_refined0.22
r_nbd_refined0.214
r_nbd_other0.211
r_symmetry_nbd_other0.204
r_nbtor_refined0.167
r_symmetry_nbd_refined0.163
r_symmetry_xyhbond_nbd_other0.108
r_symmetry_nbtor_other0.085
r_chiral_restr0.065
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_gen_planes_other0.004
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4784
Nucleic Acid Atoms
Solvent Atoms395
Heterogen Atoms89

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing