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Crystal structure of DelP123_Msd in complex with 5-azauracil
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XKO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1M Bis-Tris pH 6.4, 20% PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.19 43.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.75 α = 90 b = 85.3 β = 102.491 c = 76.46 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 PILATUS 6M 2022-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.538 74.66 99.2 0.99 11.69 5.6 86243
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.538 1.578 0.84
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 1.538 74.65 86239 4298 99.218 0.178 0.1763 0.1909 0.2087 0.2215 17.242
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] 1.645 -0.775 -0.781 -0.474
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.568 r_dihedral_angle_3_deg 13.523 r_dihedral_angle_2_deg 7.346 r_dihedral_angle_1_deg 5.584 r_lrange_it 4.986 r_lrange_other 4.959 r_scangle_it 4.293 r_scangle_other 4.292 r_scbond_it 2.801 r_scbond_other 2.801
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.568 r_dihedral_angle_3_deg 13.523 r_dihedral_angle_2_deg 7.346 r_dihedral_angle_1_deg 5.584 r_lrange_it 4.986 r_lrange_other 4.959 r_scangle_it 4.293 r_scangle_other 4.292 r_scbond_it 2.801 r_scbond_other 2.801 r_mcangle_it 2.351 r_mcangle_other 2.351 r_mcbond_it 1.638 r_mcbond_other 1.619 r_angle_refined_deg 1.611 r_angle_other_deg 0.546 r_symmetry_nbd_refined 0.442 r_nbd_other 0.31 r_nbd_refined 0.237 r_symmetry_nbd_other 0.211 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.155 r_symmetry_xyhbond_nbd_refined 0.126 r_metal_ion_refined 0.115 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.08 r_symmetry_xyhbond_nbd_other 0.025 r_gen_planes_refined 0.01 r_bond_refined_d 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4719 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing