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Crystal structure of yak lactoperoxidase with disordered heme moiety at 2.50 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 2.5 50.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.82 α = 90 b = 84.71 β = 90 c = 99.04 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 2019-09-09 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 2.5 64.38 100 0.2 0.99 7.5 11.6 23901
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 2.5 2.6 100 0.845 0.818 2.7 11.3
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 2.5 64.375 23818 1136 99.866 0.187 0.1846 0.1909 0.2394 0.2395 33.275
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] -2.347 -1.193 3.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.693 r_dihedral_angle_3_deg 18.624 r_dihedral_angle_4_deg 15.566 r_lrange_it 8.936 r_lrange_other 8.935 r_dihedral_angle_1_deg 7.544 r_mcangle_other 4.876 r_mcangle_it 4.87 r_scangle_it 4.809 r_scangle_other 4.808
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.693 r_dihedral_angle_3_deg 18.624 r_dihedral_angle_4_deg 15.566 r_lrange_it 8.936 r_lrange_other 8.935 r_dihedral_angle_1_deg 7.544 r_mcangle_other 4.876 r_mcangle_it 4.87 r_scangle_it 4.809 r_scangle_other 4.808 r_mcbond_it 2.899 r_mcbond_other 2.853 r_scbond_it 2.846 r_scbond_other 2.846 r_angle_refined_deg 1.587 r_angle_other_deg 1.229 r_symmetry_xyhbond_nbd_refined 0.551 r_symmetry_nbd_refined 0.321 r_metal_ion_refined 0.312 r_nbd_other 0.29 r_nbd_refined 0.238 r_symmetry_nbd_other 0.205 r_xyhbond_nbd_refined 0.183 r_nbtor_refined 0.166 r_symmetry_xyhbond_nbd_other 0.085 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4770 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms 147
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling MOLREP phasing