☰ Navigation Tabs
Crystal structure of native yak lactoperoxidase at 2.28 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7D52
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 0.05M potassium fluoride, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.46 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.162 α = 90 b = 85.242 β = 90 c = 96.443 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 PIXEL DECTRIS EIGER X 16M 2020-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.9677 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.28 42.621 99 0.15 0.99 7 7 30344 42.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.28 2.34 93 0.99 0.79 2.28
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 7D52 2.28 42.62 30343 770 98.513 0.176 0.1742 0.1741 0.2434 0.2432 50.639
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] -3.004 -0.967 3.971
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.665 r_dihedral_angle_4_deg 17.247 r_dihedral_angle_3_deg 16.748 r_lrange_it 13.924 r_scangle_it 7.46 r_mcangle_it 6.966 r_dihedral_angle_1_deg 6.836 r_scbond_it 4.936 r_mcbond_it 4.387 r_angle_refined_deg 1.533
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.665 r_dihedral_angle_4_deg 17.247 r_dihedral_angle_3_deg 16.748 r_lrange_it 13.924 r_scangle_it 7.46 r_mcangle_it 6.966 r_dihedral_angle_1_deg 6.836 r_scbond_it 4.936 r_mcbond_it 4.387 r_angle_refined_deg 1.533 r_nbtor_refined 0.313 r_symmetry_nbd_refined 0.27 r_symmetry_xyhbond_nbd_refined 0.229 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.172 r_chiral_restr 0.117 r_metal_ion_refined 0.077 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4770 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing