☰ Navigation Tabs
Y345F 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 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 1.93 36.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.022 α = 90 b = 67.788 β = 105.66 c = 73.024 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) 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 1.23 70.32 97.8 0.093 0.116 0.07 0.996 8.2 4.8 191400
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 1.23 1.25 0.944 1.267 0.836 0.357 2.8
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 1.23 70.32 181802 9535 97.77 0.13444 0.13317 0.138 0.15875 0.1635 RANDOM 12.368
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] -0.64 0.37 -1.27 1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.44 r_dihedral_angle_2_deg 10.86 r_dihedral_angle_1_deg 6.786 r_rigid_bond_restr 3.863 r_long_range_B_refined 3.429 r_long_range_B_other 2.657 r_angle_refined_deg 1.748 r_scangle_other 1.712 r_mcangle_it 1.343 r_mcangle_other 1.343
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.44 r_dihedral_angle_2_deg 10.86 r_dihedral_angle_1_deg 6.786 r_rigid_bond_restr 3.863 r_long_range_B_refined 3.429 r_long_range_B_other 2.657 r_angle_refined_deg 1.748 r_scangle_other 1.712 r_mcangle_it 1.343 r_mcangle_other 1.343 r_scbond_other 1.284 r_scbond_it 1.283 r_mcbond_it 0.973 r_mcbond_other 0.972 r_angle_other_deg 0.624 r_chiral_restr 0.097 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.005 r_bond_other_d 0.002 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 5599 Nucleic Acid Atoms Solvent Atoms 997 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data reduction Aimless data scaling REFMAC phasing