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Crystal structure of yak lactoperoxidase with a disordered propionic group of heme moiety at 2.20 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BXI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 0.2M potassium fluoride, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.51 51.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.98 α = 90 b = 85.08 β = 90 c = 98.93 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M mirror 2019-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.2 85 100 0.2 0.993 10.2 12 35006
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) Redundancy Number Unique Reflections (All) 1 2.2 2.27 99.9 0.99 0.967 3.1 11
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3BXI 2.2 62.274 34747 1806 99.416 0.193 0.1902 0.1902 0.2498 0.2498 28.912
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] 0.031 -0.041 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.997 r_dihedral_angle_4_deg 16.894 r_dihedral_angle_3_deg 15.309 r_lrange_it 8.505 r_dihedral_angle_1_deg 7.161 r_scangle_it 4.385 r_mcangle_it 3.99 r_scbond_it 2.83 r_mcbond_it 2.412 r_angle_refined_deg 1.522
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.997 r_dihedral_angle_4_deg 16.894 r_dihedral_angle_3_deg 15.309 r_lrange_it 8.505 r_dihedral_angle_1_deg 7.161 r_scangle_it 4.385 r_mcangle_it 3.99 r_scbond_it 2.83 r_mcbond_it 2.412 r_angle_refined_deg 1.522 r_metal_ion_refined 0.321 r_nbtor_refined 0.314 r_symmetry_xyhbond_nbd_refined 0.266 r_nbd_refined 0.224 r_symmetry_nbd_refined 0.201 r_xyhbond_nbd_refined 0.186 r_chiral_restr 0.114 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4770 Nucleic Acid Atoms Solvent Atoms 450 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling MOLREP phasing