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Phytophthora nicotianae var. parasitica NADAR in complex with ADP-ribose
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 7.5 294 0.1 M Sodium HEPES pH 7.5, 20% (w/v) PEG10000
Crystal Properties Matthews coefficient Solvent content 2.49 50.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.829 α = 90 b = 66.593 β = 90 c = 72.888 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 100 PIXEL DECTRIS EIGER2 XE 16M 2022-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97629 Diamond I03
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 1.6 49.212 100 0.072 0.077 0.024 1 13 9.6 29538
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 1.6 1.63 2.128 2.246 0.712 0.596 0.9 9.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 AlphaFold 1.6 49.212 29479 1425 99.959 0.199 0.1976 0.2053 0.2279 0.2353 31.797
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] -1.493 -1.001 2.494
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.364 r_dihedral_angle_3_deg 14.097 r_dihedral_angle_2_deg 9.578 r_lrange_it 7.173 r_lrange_other 7.169 r_scangle_it 6.082 r_scangle_other 6.079 r_dihedral_angle_1_deg 5.939 r_scbond_it 4.325 r_scbond_other 4.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.364 r_dihedral_angle_3_deg 14.097 r_dihedral_angle_2_deg 9.578 r_lrange_it 7.173 r_lrange_other 7.169 r_scangle_it 6.082 r_scangle_other 6.079 r_dihedral_angle_1_deg 5.939 r_scbond_it 4.325 r_scbond_other 4.323 r_mcangle_it 3.343 r_mcangle_other 3.341 r_mcbond_it 2.744 r_mcbond_other 2.744 r_angle_refined_deg 1.907 r_angle_other_deg 0.653 r_symmetry_nbd_refined 0.245 r_nbd_other 0.229 r_nbd_refined 0.223 r_nbtor_refined 0.191 r_symmetry_nbd_other 0.185 r_symmetry_xyhbond_nbd_refined 0.128 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.094 r_symmetry_nbtor_other 0.077 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1536 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing