Navigation Tabs SFX Ferric structure of Y389F variant of A type dye-decolourising peroxidase DtpAa
Serial Crystallography (SX)
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 7 293 1:1 v/v ratio of a solution containing 6.2 mg/ml Y389F DtpAa in 20 mM sodium phosphate, 150 mM NaCl pH 7 with a precipitant solution consisting of 100 mM HEPES pH 7 and 15% PEG 6000 to give a final volume of 400 ul.
Crystal Properties Matthews coefficient Solvent content 2 38.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.567 α = 90 b = 68.14 β = 105.5 c = 74.8 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 293 CCD RAYONIX MX225-HS 2022-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL2 1.13 SACLA BL2
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
Fixed Target Diffraction ID Description Sample Holding Support Base Motion control Details Sample Solvent 1 Silicon chip
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 10 (fs) 30 11 (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 11101
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.7 48.85 100 0.879 0.279 3.13 70.4 73582
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 0.514 0.753
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 1.7 48.85 73582 3803 99.99 0.1688 0.16695 0.1775 0.20502 0.2117 RANDOM 18.05
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 -0.06 -0.37 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.383 r_dihedral_angle_3_deg 13.69 r_dihedral_angle_1_deg 6.74 r_long_range_B_refined 5.225 r_long_range_B_other 5.217 r_scangle_other 4.779 r_scbond_other 3.34 r_scbond_it 3.339 r_mcangle_other 2.929 r_mcangle_it 2.927
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.383 r_dihedral_angle_3_deg 13.69 r_dihedral_angle_1_deg 6.74 r_long_range_B_refined 5.225 r_long_range_B_other 5.217 r_scangle_other 4.779 r_scbond_other 3.34 r_scbond_it 3.339 r_mcangle_other 2.929 r_mcangle_it 2.927 r_mcbond_it 2.24 r_mcbond_other 2.219 r_angle_refined_deg 1.924 r_angle_other_deg 0.649 r_chiral_restr 0.097 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5510 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling REFMAC phasing
