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Crystal structure of yak lactoperoxidase at 2.27 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 AMMONIUM IODIDE, 20% PEG 3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, 298K
Crystal Properties Matthews coefficient Solvent content 2.42 49.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.08 α = 90 b = 80.64 β = 102.8 c = 76.13 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 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 2.27 52.792 100 0.084 0.994 7.6 3.8 29600
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 2.27 2.34 100 0.663 0.806 1.3 3.8
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 2.27 52.79 29579 1020 99.976 0.198 0.1955 0.2094 0.2663 0.269 54.465
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] -1.586 3.455 -3.931 3.578
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.897 r_dihedral_angle_3_deg 18.817 r_dihedral_angle_4_deg 17.242 r_lrange_it 11.53 r_lrange_other 11.53 r_dihedral_angle_1_deg 7.875 r_mcangle_other 6.436 r_mcangle_it 6.435 r_scangle_other 5.81 r_scangle_it 5.806
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.897 r_dihedral_angle_3_deg 18.817 r_dihedral_angle_4_deg 17.242 r_lrange_it 11.53 r_lrange_other 11.53 r_dihedral_angle_1_deg 7.875 r_mcangle_other 6.436 r_mcangle_it 6.435 r_scangle_other 5.81 r_scangle_it 5.806 r_mcbond_it 4.236 r_mcbond_other 4.195 r_scbond_it 3.843 r_scbond_other 3.827 r_angle_refined_deg 1.593 r_angle_other_deg 1.208 r_symmetry_nbd_refined 0.292 r_nbd_other 0.286 r_symmetry_xyhbond_nbd_refined 0.268 r_xyhbond_nbd_refined 0.231 r_nbd_refined 0.211 r_symmetry_nbd_other 0.205 r_nbtor_refined 0.169 r_chiral_restr_other 0.139 r_symmetry_xyhbond_nbd_other 0.094 r_symmetry_nbtor_other 0.083 r_metal_ion_refined 0.071 r_chiral_restr 0.065 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 4763 Nucleic Acid Atoms Solvent Atoms 358 Heterogen Atoms 143
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling MOLREP phasing