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Crystal structure of yak lactoperoxidase at 1.55 A resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BYZ
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 2.13 42.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.91 α = 90 b = 78.98 β = 92.96 c = 67.82 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 225 mm CCD 2019-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.97 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 1.55 44.53 98.4 0.107 0.067 0.99 7.6 3.3 81152
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 1.55 1.58 92.8 0.934 0.604 0.44 1.1
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 7BYZ 1.55 43.247 81012 1676 98.406 0.187 0.1865 0.1949 0.226 0.228 19.578
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] -0.008 -0.015 -0.005 0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.661 r_dihedral_angle_4_deg 15.935 r_dihedral_angle_3_deg 13.28 r_dihedral_angle_1_deg 7.408 r_lrange_it 5.791 r_lrange_other 5.79 r_mcangle_it 3.165 r_mcangle_other 3.165 r_scangle_it 3.095 r_scangle_other 3.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.661 r_dihedral_angle_4_deg 15.935 r_dihedral_angle_3_deg 13.28 r_dihedral_angle_1_deg 7.408 r_lrange_it 5.791 r_lrange_other 5.79 r_mcangle_it 3.165 r_mcangle_other 3.165 r_scangle_it 3.095 r_scangle_other 3.094 r_scbond_it 2.01 r_scbond_other 2.01 r_mcbond_it 1.975 r_mcbond_other 1.934 r_angle_refined_deg 1.622 r_angle_other_deg 1.491 r_symmetry_metal_ion_refined 0.774 r_nbd_other 0.474 r_symmetry_nbd_refined 0.461 r_symmetry_xyhbond_nbd_refined 0.254 r_nbd_refined 0.215 r_xyhbond_nbd_other 0.199 r_symmetry_nbd_other 0.194 r_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.172 r_symmetry_nbtor_other 0.097 r_metal_ion_refined 0.095 r_chiral_restr 0.085 r_symmetry_xyhbond_nbd_other 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4770 Nucleic Acid Atoms Solvent Atoms 622 Heterogen Atoms 226
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing