☰ Navigation Tabs
pVHL:EloB:EloC in complex with (2S,4R)-1-((2S,4R)-1-acetyl-4-hydroxypyrrolidine-2-carbonyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 10)
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 48.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.402 α = 90 b = 93.402 β = 90 c = 364.322 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 93.402 100 0.146 0.165 0.053 9 9.5 64415 64415
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 2.4 2.53 100 0.732 0.732 0.277 1 8.9 9215
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 2.4 93.4 61092 3237 99.88 0.2275 0.2249 0.2293 0.2749 0.275 RANDOM 44.258
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] 0.24 0.24 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.967 r_dihedral_angle_4_deg 17.547 r_dihedral_angle_3_deg 14.103 r_dihedral_angle_1_deg 5.934 r_mcangle_it 2.606 r_mcbond_it 1.519 r_mcbond_other 1.519 r_angle_refined_deg 1.195 r_angle_other_deg 0.746 r_chiral_restr 0.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.967 r_dihedral_angle_4_deg 17.547 r_dihedral_angle_3_deg 14.103 r_dihedral_angle_1_deg 5.934 r_mcangle_it 2.606 r_mcbond_it 1.519 r_mcbond_other 1.519 r_angle_refined_deg 1.195 r_angle_other_deg 0.746 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10545 Nucleic Acid Atoms Solvent Atoms 382 Heterogen Atoms 132
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling XSCALE data reduction