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pVHL:EloB:EloC in complex with modified VH032 containing (3R,4S)-3-fluoro-4-hydroxyproline (ligand 14a)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NVV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 291 PEG 3350, MgOAc, Sodium cacodylate, DTT
Crystal Properties Matthews coefficient Solvent content 2.44 49.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.115 α = 90 b = 94.115 β = 90 c = 367.972 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 2016-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9282 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 49.36 99.9 0.149 0.159 0.054 0.997 8.2 8.7 46704
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.79 99.8 0.76 0.813 0.285 0.815 8
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 5NVV 2.7 49.36 44252 2380 99.76 0.2022 0.1991 0.2047 0.2584 0.2617 RANDOM 51.899
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] -0.32 -0.32 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.365 r_dihedral_angle_4_deg 15.507 r_dihedral_angle_3_deg 14.566 r_dihedral_angle_1_deg 5.793 r_angle_refined_deg 1.176 r_angle_other_deg 0.756 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.365 r_dihedral_angle_4_deg 15.507 r_dihedral_angle_3_deg 14.566 r_dihedral_angle_1_deg 5.793 r_angle_refined_deg 1.176 r_angle_other_deg 0.756 r_chiral_restr 0.062 r_bond_refined_d 0.007 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 10626 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 136
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction