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pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-((S)-2-acetamido-3,3-dimethylbutanamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 15)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VCB PDB entry 1VCB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.3 291 PEG 3350, MgOAc, Sodium cacodylate, DTT
Crystal Properties Matthews coefficient Solvent content 2.39 48.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.825 α = 90 b = 93.825 β = 90 c = 362.612 γ = 90
Symmetry Space Group P 41 2 2
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-F 2013-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 0.991 93.825 98.3 0.082 0.095 0.035 13.5 6.5 81578 81578
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 99.4 0.91 0.91 0.388 0.8 6.4 11880
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 PDB entry 1VCB 2.2 93.82 77450 4128 97.63 0.2058 0.2038 0.2077 0.243 0.2435 RANDOM 49.505
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] 0.32 0.32 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.432 r_dihedral_angle_4_deg 17.054 r_dihedral_angle_3_deg 13.701 r_dihedral_angle_1_deg 6.047 r_mcangle_it 3.173 r_mcbond_it 1.945 r_mcbond_other 1.944 r_angle_refined_deg 1.284 r_angle_other_deg 0.774 r_chiral_restr 0.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.432 r_dihedral_angle_4_deg 17.054 r_dihedral_angle_3_deg 13.701 r_dihedral_angle_1_deg 6.047 r_mcangle_it 3.173 r_mcbond_it 1.945 r_mcbond_other 1.944 r_angle_refined_deg 1.284 r_angle_other_deg 0.774 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10524 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 164
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling XSCALE data reduction