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Crystal structure of the S.pombe Ars2-Red1 complex.
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 8 278.15 200mM Ammonium Formate, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 3.46 64.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.67 α = 90 b = 128.281 β = 108.08 c = 89.261 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 R 4M 2021-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9677 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.77 84.85 76 0.29 0.98 5.3 5.56 26786
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 2.771 2.994 18.4 0.55 1.5 6.2
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT alpafold 2.77 84.85 25473 1313 76.04 0.2314 0.228 0.2338 0.2977 0.296 RANDOM 52.291
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] -0.47 -0.42 0.54 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.291 r_dihedral_angle_3_deg 16.709 r_dihedral_angle_4_deg 8.267 r_dihedral_angle_1_deg 6.513 r_angle_refined_deg 1.375 r_angle_other_deg 1.163 r_chiral_restr 0.05 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.291 r_dihedral_angle_3_deg 16.709 r_dihedral_angle_4_deg 8.267 r_dihedral_angle_1_deg 6.513 r_angle_refined_deg 1.375 r_angle_other_deg 1.163 r_chiral_restr 0.05 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7172 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction autoPROC data reduction PHASER phasing