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pVHL54-213-EloB-EloC complex_(2S,4R)-4-hydroxy-1-(2-(3-methylisoxazol- 5-yl)acetyl)-N-(4-nitrobenzyl)pyrrolidine-2-carboxamide bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZRF PDB ENTRY 3ZRF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1 M NA CITRATE PH 5.8, 0.2 M MG ACETATE, 15% PEG 8000, 50 MM DTT.
Crystal Properties Matthews coefficient Solvent content 2.66 53.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.404 α = 90 b = 93.404 β = 90 c = 362.891 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 CCD ADSC QUANTUM 315r 2010-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 SOLEIL PROXIMA 1
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 2.5 45 99.5 0.14 10.04 6.3 56353 3 53.2
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 2.5 2.66 98.6 0.52 2.85 5.4
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 PDB ENTRY 3ZRF 2.5 41.5 53932 2417 99.75 0.23235 0.22894 0.2257 0.30152 0.2925 RANDOM 35.35
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.571 r_dihedral_angle_4_deg 22.599 r_dihedral_angle_3_deg 18.783 r_dihedral_angle_1_deg 7.263 r_scangle_it 3.344 r_scbond_it 1.995 r_angle_refined_deg 1.63 r_mcangle_it 1.471 r_mcbond_it 0.76 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.571 r_dihedral_angle_4_deg 22.599 r_dihedral_angle_3_deg 18.783 r_dihedral_angle_1_deg 7.263 r_scangle_it 3.344 r_scbond_it 1.995 r_angle_refined_deg 1.63 r_mcangle_it 1.471 r_mcbond_it 0.76 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10268 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing