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pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(3-methyl-4-(thiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 6)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 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 2.38 48.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.487 α = 90 b = 93.487 β = 90 c = 363.891 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 2014-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.7 48.9 99.9 0.158 6.9 6.5 45646
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.85 100 0.638 2 6.7
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 1VCB 2.7 93.49 43222 2327 99.77 0.2238 0.2216 0.2238 0.2638 0.2588 RANDOM 45.456
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] -0.04 -0.04 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.722 r_dihedral_angle_4_deg 14.861 r_dihedral_angle_3_deg 13.128 r_dihedral_angle_1_deg 5.544 r_mcangle_it 1.845 r_angle_refined_deg 1.046 r_mcbond_it 1.03 r_mcbond_other 1.03 r_angle_other_deg 0.735 r_chiral_restr 0.054
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.722 r_dihedral_angle_4_deg 14.861 r_dihedral_angle_3_deg 13.128 r_dihedral_angle_1_deg 5.544 r_mcangle_it 1.845 r_angle_refined_deg 1.046 r_mcbond_it 1.03 r_mcbond_other 1.03 r_angle_other_deg 0.735 r_chiral_restr 0.054 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10508 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 116
Software Software Software Name Purpose XDS data reduction REFMAC refinement PDB_EXTRACT data extraction SCALA data scaling XSCALE data scaling XSCALE data reduction