7C73

Crystal structure of yak lactoperoxidase using data obtained from crystals soaked in MgCl2 at 2.70 A resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.82980.2M CaCl2, 20% PEG 3350, tris-HCl, pH 8
Crystal Properties
Matthews coefficientSolvent content
2.3748

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.88α = 90
b = 79.93β = 101.35
c = 75.05γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRROR2019-12-09MSINGLE 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 Merge 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
12.750980.1980.9653.117274
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.8396.80.960.5363

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-VALUE6LNV2.747.5771685684397.580.2220.2180.306335.678
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]
-0.042-0.0710.0390.029
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.68
r_dihedral_angle_3_deg20.398
r_dihedral_angle_4_deg16.2
r_lrange_it10.506
r_lrange_other10.499
r_dihedral_angle_1_deg9.558
r_mcangle_it3.644
r_mcangle_other3.643
r_scangle_it2.982
r_scangle_other2.982
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.68
r_dihedral_angle_3_deg20.398
r_dihedral_angle_4_deg16.2
r_lrange_it10.506
r_lrange_other10.499
r_dihedral_angle_1_deg9.558
r_mcangle_it3.644
r_mcangle_other3.643
r_scangle_it2.982
r_scangle_other2.982
r_mcbond_it2.061
r_mcbond_other2.056
r_scbond_it1.676
r_scbond_other1.676
r_angle_refined_deg1.664
r_angle_other_deg1.224
r_nbd_other0.271
r_nbd_refined0.248
r_symmetry_xyhbond_nbd_refined0.234
r_symmetry_nbd_other0.209
r_xyhbond_nbd_refined0.205
r_symmetry_nbd_refined0.2
r_nbtor_refined0.174
r_symmetry_xyhbond_nbd_other0.095
r_symmetry_nbtor_other0.083
r_chiral_restr0.074
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4817
Nucleic Acid Atoms
Solvent Atoms242
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing