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Crystal structure of potassium induced heme modification in yak lactoperoxidase at 2.30 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 2.49 50.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.7 α = 90 b = 84.71 β = 90 c = 98.75 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 CCD MARRESEARCH mirror 2019-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.97947 RRCAT INDUS-2 PX-BL21
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 2.3 58.114 100 0.2 0.98 5.9 6.8 30425
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 2.3 2.39 99.9 0.85 0.88 1.9 6.5
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 2.3 58.11 30367 663 99.947 0.191 0.1903 0.1952 0.2442 0.2478 27.013
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] -1.087 -1.05 2.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.892 r_dihedral_angle_3_deg 19.183 r_dihedral_angle_4_deg 14.384 r_lrange_it 8.601 r_lrange_other 8.576 r_dihedral_angle_1_deg 7.694 r_mcangle_other 4.307 r_mcangle_it 4.305 r_scangle_it 4.019 r_scangle_other 4.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.892 r_dihedral_angle_3_deg 19.183 r_dihedral_angle_4_deg 14.384 r_lrange_it 8.601 r_lrange_other 8.576 r_dihedral_angle_1_deg 7.694 r_mcangle_other 4.307 r_mcangle_it 4.305 r_scangle_it 4.019 r_scangle_other 4.019 r_mcbond_it 2.522 r_mcbond_other 2.505 r_scbond_other 2.464 r_scbond_it 2.463 r_angle_refined_deg 1.651 r_angle_other_deg 1.251 r_metal_ion_refined 0.371 r_nbd_refined 0.25 r_symmetry_xyhbond_nbd_refined 0.243 r_nbd_other 0.221 r_symmetry_nbd_other 0.208 r_xyhbond_nbd_refined 0.194 r_symmetry_nbd_refined 0.174 r_nbtor_refined 0.168 r_symmetry_xyhbond_nbd_other 0.138 r_symmetry_metal_ion_refined 0.086 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.078 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4784 Nucleic Acid Atoms Solvent Atoms 329 Heterogen Atoms 117
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling MOLREP phasing