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Crystal structure of yak lactoperoxidase at 1.93 A resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6A4Y
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 42.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.85 α = 90 b = 78.92 β = 92.95 c = 67.75 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 0.98 RRCAT INDUS-2 PX-BL21
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.93 53.84 100 0.066 0.078 0.04 0.996 14.3 3.7 42433
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 1.98 100 0.218 0.258 0.136 0.935 5 3.5
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 6A4Y 1.933 53.837 42433 1503 99.991 0.147 0.1453 0.1549 0.1979 0.2056 19.698
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] -0.029 -0.865 -0.207 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.536 r_dihedral_angle_3_deg 17.149 r_dihedral_angle_4_deg 16.979 r_dihedral_angle_1_deg 8.117 r_lrange_it 6.992 r_lrange_other 6.991 r_mcangle_it 3.871 r_mcangle_other 3.863 r_scangle_it 3.284 r_scangle_other 3.284
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.536 r_dihedral_angle_3_deg 17.149 r_dihedral_angle_4_deg 16.979 r_dihedral_angle_1_deg 8.117 r_lrange_it 6.992 r_lrange_other 6.991 r_mcangle_it 3.871 r_mcangle_other 3.863 r_scangle_it 3.284 r_scangle_other 3.284 r_mcbond_it 2.265 r_mcbond_other 2.244 r_scbond_it 2.032 r_scbond_other 2.031 r_angle_refined_deg 1.69 r_angle_other_deg 1.355 r_nbd_other 0.244 r_nbd_refined 0.241 r_chiral_restr_other 0.221 r_symmetry_nbd_refined 0.216 r_symmetry_nbd_other 0.202 r_xyhbond_nbd_refined 0.198 r_metal_ion_refined 0.197 r_nbtor_refined 0.168 r_symmetry_xyhbond_nbd_refined 0.152 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.01 r_symmetry_xyhbond_nbd_other 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.006 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4760 Nucleic Acid Atoms Solvent Atoms 637 Heterogen Atoms 280
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing Coot model building