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Y345F/F347Y/Y389F Variant of Dye Type Peroxidase Aa (DtpAa) from Streptomyces lividans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TB8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 1:1 RATIO OF A 15 MG/ML PROTEIN SOLUTION WITH A PRECIPITANT SOLUTION CONTAINING 20% PEG 6000, 100 MM HEPES PH 7.0
Crystal Properties Matthews coefficient Solvent content 1.97 37.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.852 α = 90 b = 67.93 β = 105.46 c = 74.483 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 PIXEL DECTRIS EIGER X 16M 2022-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.98 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.5 58.26 100 0.078 0.092 0.049 0.999 10.9 6.9 110533
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 1.336 1.582 0.84 0.558 6.9
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 (Observed) 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 1.5 58.26 105042 5468 100 0.1622 0.16078 0.1684 0.18922 0.1982 RANDOM 18.962
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] 0.28 0.12 -1.2 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.43 r_dihedral_angle_3_deg 13.115 r_dihedral_angle_1_deg 6.991 r_long_range_B_refined 5.408 r_long_range_B_other 5.364 r_scangle_other 4.396 r_scbond_other 3.194 r_scbond_it 3.193 r_mcangle_other 2.915 r_mcangle_it 2.914
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.43 r_dihedral_angle_3_deg 13.115 r_dihedral_angle_1_deg 6.991 r_long_range_B_refined 5.408 r_long_range_B_other 5.364 r_scangle_other 4.396 r_scbond_other 3.194 r_scbond_it 3.193 r_mcangle_other 2.915 r_mcangle_it 2.914 r_mcbond_it 2.239 r_mcbond_other 2.237 r_angle_refined_deg 2.005 r_angle_other_deg 0.685 r_chiral_restr 0.1 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_gen_planes_other 0.005 r_bond_other_d 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5579 Nucleic Acid Atoms Solvent Atoms 648 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction Aimless data scaling REFMAC phasing