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pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(oxazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 2)
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 2.41 48.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.779 α = 90 b = 93.779 β = 90 c = 366.034 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 CCD ADSC QUANTUM 315r 2013-08-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9393 ESRF ID14-4
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 93.779 98.9 0.098 0.113 0.038 12.8 7.3 83149 83149
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 99.9 0.687 0.687 0.264 1.1 7.4 12076
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 2.2 93.779 78834 4195 98.53 0.2085 0.2062 0.2102 0.2509 0.2531 RANDOM 39.099
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] -0.18 -0.18 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.401 r_dihedral_angle_4_deg 19.21 r_dihedral_angle_3_deg 13.714 r_dihedral_angle_1_deg 6.097 r_mcangle_it 2.552 r_mcbond_it 1.514 r_mcbond_other 1.514 r_angle_refined_deg 1.248 r_angle_other_deg 0.788 r_chiral_restr 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.401 r_dihedral_angle_4_deg 19.21 r_dihedral_angle_3_deg 13.714 r_dihedral_angle_1_deg 6.097 r_mcangle_it 2.552 r_mcbond_it 1.514 r_mcbond_other 1.514 r_angle_refined_deg 1.248 r_angle_other_deg 0.788 r_chiral_restr 0.071 r_bond_refined_d 0.008 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 10530 Nucleic Acid Atoms Solvent Atoms 526 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