☰ Navigation Tabs
Crystal structure of yak lactoperoxidase using data obtained from crystals soaked in MgCl2 at 2.70 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LNV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 0.2M CaCl2, 20% PEG 3350, tris-HCl, pH 8
Crystal Properties Matthews coefficient Solvent content 2.37 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.88 α = 90 b = 79.93 β = 101.35 c = 75.05 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 MIRROR 2019-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.97947 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 2.7 50 98 0.198 0.96 5 3.1 17274
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 2.7 2.83 96.8 0.96 0.536 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 6LNV 2.7 47.577 16856 843 97.58 0.222 0.218 0.2201 0.3063 0.3078 35.678
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] -0.042 -0.071 0.039 0.029
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.68 r_dihedral_angle_3_deg 20.398 r_dihedral_angle_4_deg 16.2 r_lrange_it 10.506 r_lrange_other 10.499 r_dihedral_angle_1_deg 9.558 r_mcangle_it 3.644 r_mcangle_other 3.643 r_scangle_it 2.982 r_scangle_other 2.982
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.68 r_dihedral_angle_3_deg 20.398 r_dihedral_angle_4_deg 16.2 r_lrange_it 10.506 r_lrange_other 10.499 r_dihedral_angle_1_deg 9.558 r_mcangle_it 3.644 r_mcangle_other 3.643 r_scangle_it 2.982 r_scangle_other 2.982 r_mcbond_it 2.061 r_mcbond_other 2.056 r_scbond_it 1.676 r_scbond_other 1.676 r_angle_refined_deg 1.664 r_angle_other_deg 1.224 r_nbd_other 0.271 r_nbd_refined 0.248 r_symmetry_xyhbond_nbd_refined 0.234 r_symmetry_nbd_other 0.209 r_xyhbond_nbd_refined 0.205 r_symmetry_nbd_refined 0.2 r_nbtor_refined 0.174 r_symmetry_xyhbond_nbd_other 0.095 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4817 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing