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Y345F/F347Y 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 7 291 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 1.91 35.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.037 α = 90 b = 68.127 β = 105.42 c = 73.046 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 2021-04-23 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) 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 1.27 70.42 99 0.066 0.999 9 5 174917
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 1.27 1.29 83 1.519 0.339 0.6 3.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.27 70.42 166396 8482 98.99 0.15372 0.15169 0.19253 0.196 RANDOM 16.731
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] 1.2 0.32 -2.32 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.951 r_dihedral_angle_2_deg 11.315 r_dihedral_angle_1_deg 6.899 r_rigid_bond_restr 5.13 r_long_range_B_refined 3.399 r_long_range_B_other 3.158 r_scangle_other 2.654 r_scbond_it 2.084 r_scbond_other 2.084 r_mcangle_it 1.966
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.951 r_dihedral_angle_2_deg 11.315 r_dihedral_angle_1_deg 6.899 r_rigid_bond_restr 5.13 r_long_range_B_refined 3.399 r_long_range_B_other 3.158 r_scangle_other 2.654 r_scbond_it 2.084 r_scbond_other 2.084 r_mcangle_it 1.966 r_mcangle_other 1.966 r_angle_refined_deg 1.842 r_mcbond_it 1.572 r_mcbond_other 1.564 r_angle_other_deg 0.655 r_chiral_restr 0.103 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5582 Nucleic Acid Atoms Solvent Atoms 689 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling REFMAC phasing