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SSX structure of dye-type peroxidase DtpB from Streptomyces lividans
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YRJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 291 6-10 mg/ml of protein in 50 mm sodium acetate, 150 mm NaCl pH 5 mixed with 150 mM MgCl2, 150 mm HEPES, 20 % PEG 4000, pH 7.5, batch mode.
Crystal Properties Matthews coefficient Solvent content 2.55 51.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.4 α = 90 b = 121.373 β = 90 c = 199.295 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL DECTRIS EIGER2 X CdTe 9M 2023-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.6200 Diamond I24
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 Oxford silicon chip Geobrick and Smaract
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 undefined (fs) undefined (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1
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 2.75 103.66 100 0.916 0.303 5.1 22.2 55276
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 2.75 2.8 0.297 1.018
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.75 79.397 55273 2784 99.989 0.193 0.1905 0.1904 0.2439 0.244 38.853
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] 0.159 0.069 -0.228
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.136 r_dihedral_angle_6_deg 11.626 r_dihedral_angle_1_deg 6.622 r_lrange_it 6.139 r_dihedral_angle_2_deg 4.316 r_scangle_it 3.59 r_mcangle_it 2.899 r_scbond_it 2.077 r_mcbond_it 1.632 r_angle_refined_deg 1.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.136 r_dihedral_angle_6_deg 11.626 r_dihedral_angle_1_deg 6.622 r_lrange_it 6.139 r_dihedral_angle_2_deg 4.316 r_scangle_it 3.59 r_mcangle_it 2.899 r_scbond_it 2.077 r_mcbond_it 1.632 r_angle_refined_deg 1.119 r_nbtor_refined 0.297 r_symmetry_nbd_refined 0.224 r_nbd_refined 0.192 r_xyhbond_nbd_refined 0.133 r_symmetry_xyhbond_nbd_refined 0.122 r_chiral_restr 0.083 r_bond_refined_d 0.003 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13935 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 260
Software Software Software Name Purpose REFMAC refinement DIALS data reduction xia2 data reduction xia2 data scaling MOLREP phasing Coot model building