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pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(thiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 4)
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 2.36 47.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.097 α = 90 b = 93.097 β = 90 c = 364.436 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 2014-04-27 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 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 0.993 93.1 99.1 0.105 0.119 0.038 14.3 8.8 50195 50195
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 2.6 2.74 99 0.962 0.962 0.355 0.8 7.9 7199
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 2.6 93.1 47544 2553 98.9 0.2085 0.2056 0.2098 0.2611 0.2596 RANDOM 52.891
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] -0.57 -0.57 1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.287 r_dihedral_angle_4_deg 16.104 r_dihedral_angle_3_deg 13.739 r_dihedral_angle_1_deg 5.916 r_mcangle_it 3.5 r_mcbond_it 2.088 r_mcbond_other 2.088 r_angle_refined_deg 1.175 r_angle_other_deg 0.759 r_chiral_restr 0.059
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.287 r_dihedral_angle_4_deg 16.104 r_dihedral_angle_3_deg 13.739 r_dihedral_angle_1_deg 5.916 r_mcangle_it 3.5 r_mcbond_it 2.088 r_mcbond_other 2.088 r_angle_refined_deg 1.175 r_angle_other_deg 0.759 r_chiral_restr 0.059 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 10520 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 112
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling XSCALE data reduction