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Survivin 1-127 in complex with a molecular tweezer-Histone-H3-peptide conjugate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UIG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 0.1M imidazole pH 8.0, 0.05M Ca-acetate, 35% v/v 2-ethoxyethanol
Crystal Properties Matthews coefficient Solvent content 2.64 53.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.549 α = 90 b = 64.091 β = 141.42 c = 75.872 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 EIGER2 X 16M 2020-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.999891 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2 49.97 96.9 0.196 0.213 0.996 9.45 6.769 20209 36.219
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 96.2 1.935 2.091 0.492 0.9 6.876
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 (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 2 49.97 19204 1011 98.04 0.2163 0.2139 0.2194 0.2629 0.2655 RANDOM 43.553
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] 2.13 1.18 -2.26 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.014 r_dihedral_angle_4_deg 22.398 r_dihedral_angle_3_deg 17.471 r_dihedral_angle_1_deg 6.419 r_mcangle_it 4.682 r_mcbond_it 3.207 r_mcbond_other 3.206 r_angle_refined_deg 2.247 r_angle_other_deg 1.236 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.014 r_dihedral_angle_4_deg 22.398 r_dihedral_angle_3_deg 17.471 r_dihedral_angle_1_deg 6.419 r_mcangle_it 4.682 r_mcbond_it 3.207 r_mcbond_other 3.206 r_angle_refined_deg 2.247 r_angle_other_deg 1.236 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1982 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 211
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing