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YdhG-like domain-containing protein (Frataxin) from Listeria monocytogenes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.3 295.15 2.5 mg/mL protein, 0.1 M MES. 10% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.27 45.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.974 α = 90 b = 51.296 β = 107.172 c = 60.583 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 EIGER2 S 9M 2023-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.8731 ESRF ID30B
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 1.72 57.88 99.9 0.173 0.188 0.072 0.966 6.9 6.8 27261 26
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 1.722 1.752 99 3.009 3.297 1.33 0.362 1.4 6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.75 57.88 26124 1296 99.752 0.182 0.1804 0.2223 0.2502 RANDOM 30.7
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] -1.986 -0.47 1.742 0.449
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.873 r_dihedral_angle_6_deg 13.682 r_dihedral_angle_2_deg 12.66 r_lrange_it 9.619 r_scangle_it 8.817 r_scbond_it 6.153 r_dihedral_angle_1_deg 5.687 r_mcangle_it 4.412 r_mcbond_it 3.46 r_angle_refined_deg 2.469
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.873 r_dihedral_angle_6_deg 13.682 r_dihedral_angle_2_deg 12.66 r_lrange_it 9.619 r_scangle_it 8.817 r_scbond_it 6.153 r_dihedral_angle_1_deg 5.687 r_mcangle_it 4.412 r_mcbond_it 3.46 r_angle_refined_deg 2.469 r_nbtor_refined 0.332 r_symmetry_nbd_refined 0.266 r_nbd_refined 0.222 r_symmetry_xyhbond_nbd_refined 0.211 r_chiral_restr 0.141 r_xyhbond_nbd_refined 0.139 r_ncsr_local_group_1 0.128 r_bond_refined_d 0.014 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1989 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 33
Software Software Software Name Purpose Aimless data scaling gemmi data extraction REFMAC refinement PHASER phasing Coot model building XDS data reduction