6L2J

Crystal structure of yak lactoperoxidase at 1.93 A resolution.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6A4Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.82980.2M AMMONIUM IODIDE, 20% PEG 3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, 298K
Crystal Properties
Matthews coefficientSolvent content
2.1342.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.85α = 90
b = 78.92β = 92.95
c = 67.75γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2019-09-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONRRCAT INDUS-2 BEAMLINE PX-BL210.98RRCAT INDUS-2PX-BL21

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.9353.841000.0660.0780.040.99614.33.742433
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.931.981000.2180.2580.1360.93553.5

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-VALUE6A4Y1.93353.83742433150399.9910.1470.14530.197919.698
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]
-0.029-0.865-0.2070.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.536
r_dihedral_angle_3_deg17.149
r_dihedral_angle_4_deg16.979
r_dihedral_angle_1_deg8.117
r_lrange_it6.992
r_lrange_other6.991
r_mcangle_it3.871
r_mcangle_other3.863
r_scangle_it3.284
r_scangle_other3.284
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.536
r_dihedral_angle_3_deg17.149
r_dihedral_angle_4_deg16.979
r_dihedral_angle_1_deg8.117
r_lrange_it6.992
r_lrange_other6.991
r_mcangle_it3.871
r_mcangle_other3.863
r_scangle_it3.284
r_scangle_other3.284
r_mcbond_it2.265
r_mcbond_other2.244
r_scbond_it2.032
r_scbond_other2.031
r_angle_refined_deg1.69
r_angle_other_deg1.355
r_nbd_other0.244
r_nbd_refined0.241
r_chiral_restr_other0.221
r_symmetry_nbd_refined0.216
r_symmetry_nbd_other0.202
r_xyhbond_nbd_refined0.198
r_metal_ion_refined0.197
r_nbtor_refined0.168
r_symmetry_xyhbond_nbd_refined0.152
r_chiral_restr0.088
r_symmetry_nbtor_other0.084
r_bond_refined_d0.01
r_symmetry_xyhbond_nbd_other0.009
r_gen_planes_refined0.008
r_gen_planes_other0.006
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4760
Nucleic Acid Atoms
Solvent Atoms637
Heterogen Atoms280

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building