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Crystal structure of DARPin-DARPin rigid fusion, variant DD_232_11_D12 in complex JNK1a1 and JIP1 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SVX 1SVX chain A and 1UKH experimental model PDB 1UKH 1SVX chain A and 1UKH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 Lithium Sulfate 1.8 M
Tris 0.1 M
Additives (0.002% w/v)
Adenosine, Pepstatin A
Epinephrine
Sodium phenyl phosphate dibasic dehydrate
Inosine 5-triphosphate trisodium salt
pH 8.5
Crystal Properties Matthews coefficient Solvent content 3.86 68.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 219.99 α = 90 b = 141.76 β = 97.83 c = 119.85 γ = 90
Symmetry Space Group C 1 2 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 2014-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000000 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.2 49.383 97.94 0.1345 0.05445 0.998 11.27 7 58948
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.314 98.46 1.842 0.7352 0.42 1.13 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1SVX chain A and 1UKH 3.2 49.383 1.35 58926 2944 97.97 0.1771 0.1753 0.2124 0.2048
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.539 f_angle_d 0.494 f_chiral_restr 0.041 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16102 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 177
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing