7C74

Crystal structure of yak lactoperoxidase using data obtained from crystals soaked in CaCl2 at 2.73 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6LO7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.82980.2M CaCl2, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3647.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.06α = 90
b = 80.59β = 101.31
c = 74.83γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDmirror2019-12-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONRRCAT INDUS-2 BEAMLINE PX-BL210.97RRCAT INDUS-2PX-BL21

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
12.7353.0199.90.1230.0790.966.53.516875
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)
12.732.81000.3140.1970.943

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-VALUE6LO72.7353.011683482699.7040.20.19530.291931.186
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]
-0.0790.029-0.2160.263
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.442
r_dihedral_angle_3_deg17.401
r_dihedral_angle_4_deg16.77
r_dihedral_angle_1_deg8.548
r_lrange_it7.636
r_lrange_other7.556
r_mcangle_other4.064
r_mcangle_it4.062
r_scangle_it3.006
r_scangle_other3.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.442
r_dihedral_angle_3_deg17.401
r_dihedral_angle_4_deg16.77
r_dihedral_angle_1_deg8.548
r_lrange_it7.636
r_lrange_other7.556
r_mcangle_other4.064
r_mcangle_it4.062
r_scangle_it3.006
r_scangle_other3.006
r_mcbond_it2.364
r_mcbond_other2.346
r_scbond_other1.683
r_scbond_it1.682
r_angle_refined_deg1.466
r_angle_other_deg1.164
r_symmetry_xyhbond_nbd_refined0.238
r_nbd_other0.205
r_nbd_refined0.203
r_xyhbond_nbd_refined0.196
r_symmetry_nbd_other0.191
r_nbtor_refined0.163
r_symmetry_nbd_refined0.154
r_symmetry_nbtor_other0.08
r_symmetry_xyhbond_nbd_other0.068
r_chiral_restr0.061
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_gen_planes_other0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4770
Nucleic Acid Atoms
Solvent Atoms316
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing