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Crystal structure of yak lactoperoxidase using data obtained from crystals soaked in CaCl2 at 2.73 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LO7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 0.2M CaCl2, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.36 47.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.06 α = 90 b = 80.59 β = 101.31 c = 74.83 γ = 90
Symmetry Space Group P 1 21 1
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 MARMOSAIC 325 mm CCD mirror 2019-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.97 RRCAT INDUS-2 PX-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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.73 53.01 99.9 0.123 0.079 0.96 6.5 3.5 16875
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) Redundancy Number Unique Reflections (All) 1 2.73 2.8 100 0.314 0.197 0.94 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 6LO7 2.73 53.01 16834 826 99.704 0.2 0.1953 0.2 0.2919 0.2922 31.186
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] -0.079 0.029 -0.216 0.263
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.442 r_dihedral_angle_3_deg 17.401 r_dihedral_angle_4_deg 16.77 r_dihedral_angle_1_deg 8.548 r_lrange_it 7.636 r_lrange_other 7.556 r_mcangle_other 4.064 r_mcangle_it 4.062 r_scangle_it 3.006 r_scangle_other 3.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.442 r_dihedral_angle_3_deg 17.401 r_dihedral_angle_4_deg 16.77 r_dihedral_angle_1_deg 8.548 r_lrange_it 7.636 r_lrange_other 7.556 r_mcangle_other 4.064 r_mcangle_it 4.062 r_scangle_it 3.006 r_scangle_other 3.006 r_mcbond_it 2.364 r_mcbond_other 2.346 r_scbond_other 1.683 r_scbond_it 1.682 r_angle_refined_deg 1.466 r_angle_other_deg 1.164 r_symmetry_xyhbond_nbd_refined 0.238 r_nbd_other 0.205 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.196 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.163 r_symmetry_nbd_refined 0.154 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.068 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 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 316 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing