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pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 5)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VBC PDB entry 1VBC
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 2.34 47.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.68 α = 90 b = 92.68 β = 90 c = 364.02 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 2012-12-18 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) 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 2.1 92.68 93841
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 100 1.303 1.355 2.66 13.4
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 1VBC 2.1 92.68 89136 4704 99.97 0.206 0.2047 0.2098 0.2291 0.2313 RANDOM 43.74
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] 0.41 0.41 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.063 r_dihedral_angle_4_deg 17.666 r_dihedral_angle_3_deg 13.669 r_dihedral_angle_1_deg 5.954 r_mcangle_it 3.153 r_mcbond_other 1.914 r_mcbond_it 1.913 r_angle_refined_deg 1.212 r_angle_other_deg 0.745 r_chiral_restr 0.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.063 r_dihedral_angle_4_deg 17.666 r_dihedral_angle_3_deg 13.669 r_dihedral_angle_1_deg 5.954 r_mcangle_it 3.153 r_mcbond_other 1.914 r_mcbond_it 1.913 r_angle_refined_deg 1.212 r_angle_other_deg 0.745 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10174 Nucleic Acid Atoms Solvent Atoms 603 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement XDS data reduction PDB_EXTRACT data extraction XSCALE data scaling XSCALE data reduction