☰ Navigation Tabs
Crystal structure of yak lactoperoxidase with partially coordinated Na ion in the distal heme cavity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6L3Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 0.2M Sodium Fluoride, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.47 50.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.91 α = 90 b = 84.83 β = 90 c = 98.56 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 PILATUS 2M mirror 2019-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.00 ELETTRA 11.2C
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 2.7 64.3 99.3 0.2 0.09 0.97 7.1 9.9 18790
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 2.7 2.77 97.6 1.05 0.34 0.83 2.8 9.3
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 6L3Z 2.7 64.295 18789 893 98.931 0.197 0.193 0.2004 0.2675 0.2683 25.515
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] 0.061 0.172 -0.233
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.907 r_dihedral_angle_3_deg 19.104 r_dihedral_angle_4_deg 15.146 r_dihedral_angle_1_deg 8.188 r_lrange_it 8.134 r_lrange_other 8.07 r_mcangle_other 4.476 r_mcangle_it 4.472 r_scangle_it 3.675 r_scangle_other 3.674
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.907 r_dihedral_angle_3_deg 19.104 r_dihedral_angle_4_deg 15.146 r_dihedral_angle_1_deg 8.188 r_lrange_it 8.134 r_lrange_other 8.07 r_mcangle_other 4.476 r_mcangle_it 4.472 r_scangle_it 3.675 r_scangle_other 3.674 r_mcbond_it 2.585 r_mcbond_other 2.549 r_scbond_other 2.098 r_scbond_it 2.097 r_angle_refined_deg 1.648 r_angle_other_deg 1.192 r_symmetry_xyhbond_nbd_refined 0.332 r_xyhbond_nbd_refined 0.22 r_nbd_refined 0.214 r_nbd_other 0.211 r_symmetry_nbd_other 0.204 r_nbtor_refined 0.167 r_symmetry_nbd_refined 0.163 r_symmetry_xyhbond_nbd_other 0.108 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4784 Nucleic Acid Atoms Solvent Atoms 395 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing