☰ Navigation Tabs
Crystal structure of hydrogen peroxide bound bovine lactoperoxidase at 2.3 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NT3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 0.2M AMMONIUM IODIDE, 20% PEG3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, 298K.
Crystal Properties Matthews coefficient Solvent content 2.39 48.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.828 α = 90 b = 80.42 β = 102.577 c = 75.823 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 2019-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.9795 RRCAT INDUS-2 PX-BL21
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 2.3 54.515 99.2 0.112 0.96 7.2 3.4 27946
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 0.495 1 2 3.3
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 THROUGHOUT 4NT3 2.3 54.46 27800 1401 98.725 0.248 0.2454 0.249 0.2951 0.2948 40.537
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] 0.617 -1.481 -1.246 1.174
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.962 r_dihedral_angle_3_deg 16.741 r_dihedral_angle_4_deg 14.093 r_dihedral_angle_1_deg 7.863 r_lrange_other 7.101 r_lrange_it 7.099 r_mcangle_it 4.7 r_mcangle_other 4.7 r_scangle_it 4.328 r_scangle_other 4.328
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.962 r_dihedral_angle_3_deg 16.741 r_dihedral_angle_4_deg 14.093 r_dihedral_angle_1_deg 7.863 r_lrange_other 7.101 r_lrange_it 7.099 r_mcangle_it 4.7 r_mcangle_other 4.7 r_scangle_it 4.328 r_scangle_other 4.328 r_mcbond_it 2.998 r_mcbond_other 2.993 r_scbond_it 2.763 r_scbond_other 2.761 r_angle_refined_deg 1.51 r_angle_other_deg 1.206 r_symmetry_metal_ion_refined 0.736 r_nbd_other 0.299 r_symmetry_xyhbond_nbd_refined 0.27 r_symmetry_nbd_refined 0.269 r_nbd_refined 0.221 r_xyhbond_nbd_refined 0.206 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.166 r_symmetry_xyhbond_nbd_other 0.123 r_symmetry_nbtor_other 0.078 r_xyhbond_nbd_other 0.075 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4774 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 119
Software Software Software Name Purpose REFMAC refinement AUTOMAR data reduction Aimless data scaling MOLREP phasing