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Re-refinement of Damage Free Ferric State of Dye Type Peroxidase Aa from Streptomyces lividans.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6I43
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 293 PEG 6K, HEPES 7.0
Crystal Properties Matthews coefficient Solvent content 2.28 46.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.95 α = 90 b = 68.3 β = 105.65 c = 74.78 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 301 CCD MPCCD 2017-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL2 1.24 SACLA BL2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Split (All) 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 1.86 41.46 100 0.0722 9.7 381 57351
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.91 0.583
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FOURIER SYNTHESIS FREE R-VALUE 1.883 40 57327 2854 99.798 0.136 0.1338 0.1464 0.1762 0.1837 29.286
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] 0.106 -0.155 -0.927 0.785
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.824 r_dihedral_angle_3_deg 14.301 r_lrange_it 7.876 r_lrange_other 7.641 r_dihedral_angle_1_deg 6.663 r_scangle_it 5.625 r_scangle_other 5.625 r_scbond_other 3.677 r_scbond_it 3.676 r_mcangle_it 3.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.824 r_dihedral_angle_3_deg 14.301 r_lrange_it 7.876 r_lrange_other 7.641 r_dihedral_angle_1_deg 6.663 r_scangle_it 5.625 r_scangle_other 5.625 r_scbond_other 3.677 r_scbond_it 3.676 r_mcangle_it 3.146 r_mcangle_other 3.146 r_dihedral_angle_2_deg 2.977 r_mcbond_it 2.349 r_mcbond_other 2.338 r_angle_refined_deg 1.72 r_angle_other_deg 0.9 r_symmetry_xyhbond_nbd_refined 0.435 r_xyhbond_nbd_refined 0.401 r_symmetry_nbd_refined 0.241 r_nbd_other 0.232 r_symmetry_nbd_other 0.21 r_nbd_refined 0.198 r_nbtor_refined 0.166 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.075 r_symmetry_xyhbond_nbd_other 0.026 r_bond_refined_d 0.015 r_gen_planes_other 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5532 Nucleic Acid Atoms Solvent Atoms 536 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling REFMAC phasing