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Reprocessing and 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 2.26 45.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.7 α = 90 b = 68.2 β = 105.6 c = 74.6 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 40 100 0.105 7.8 392 59164
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 0.416
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.86 35.476 59136 3135 99.953 0.146 0.1446 0.1568 0.1722 0.1829 RANDOM 26.839
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] -0.026 0.032 -0.014 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.358 r_dihedral_angle_3_deg 13.981 r_lrange_it 11.396 r_lrange_other 10.589 r_dihedral_angle_2_deg 8.508 r_dihedral_angle_1_deg 6.524 r_scangle_it 5.998 r_scangle_other 5.998 r_scbond_other 3.875 r_scbond_it 3.874
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.358 r_dihedral_angle_3_deg 13.981 r_lrange_it 11.396 r_lrange_other 10.589 r_dihedral_angle_2_deg 8.508 r_dihedral_angle_1_deg 6.524 r_scangle_it 5.998 r_scangle_other 5.998 r_scbond_other 3.875 r_scbond_it 3.874 r_mcangle_other 3.179 r_mcangle_it 3.177 r_mcbond_it 2.341 r_mcbond_other 2.322 r_angle_refined_deg 1.579 r_angle_other_deg 0.543 r_xyhbond_nbd_refined 0.332 r_symmetry_xyhbond_nbd_refined 0.32 r_symmetry_nbd_refined 0.289 r_nbd_other 0.213 r_nbd_refined 0.212 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.181 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5534 Nucleic Acid Atoms Solvent Atoms 540 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement CrystFEL data scaling CrystFEL data reduction PHASER phasing