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The Crystal Structure of PARP5A from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DVI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1M Ammonium Tartrate, 16% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.36 47.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.674 α = 90 b = 52.179 β = 93.842 c = 68.089 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 9M 2023-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.95373 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 48.082 98.3 0.082 10.8 4.8 48348
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 0.69
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 1.7 48.082 48329 2553 98.05 0.19 0.1888 0.198 0.2084 0.2195 25.156
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] 0.277 1.13 0.071 -0.496
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.274 r_dihedral_angle_3_deg 12.87 r_dihedral_angle_4_deg 10.801 r_dihedral_angle_1_deg 6.754 r_lrange_it 6.214 r_lrange_other 6.112 r_scangle_it 3.47 r_scangle_other 3.469 r_mcangle_it 3.009 r_mcangle_other 3.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.274 r_dihedral_angle_3_deg 12.87 r_dihedral_angle_4_deg 10.801 r_dihedral_angle_1_deg 6.754 r_lrange_it 6.214 r_lrange_other 6.112 r_scangle_it 3.47 r_scangle_other 3.469 r_mcangle_it 3.009 r_mcangle_other 3.008 r_scbond_it 2.113 r_scbond_other 2.113 r_mcbond_other 1.834 r_mcbond_it 1.833 r_angle_refined_deg 1.373 r_angle_other_deg 1.302 r_nbd_other 0.242 r_nbd_refined 0.199 r_symmetry_nbd_refined 0.183 r_symmetry_nbd_other 0.178 r_symmetry_xyhbond_nbd_refined 0.165 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.148 r_ncsr_local_group_1 0.103 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3357 Nucleic Acid Atoms Solvent Atoms 425 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing