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CRYSTAL STRUCTURE OF NEDD4 WITH A UB VARIANT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZNV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 The NEDD4 and Ubiquitin Variant was mixed at molar ratio ~1:2, and then concentrated to 15mg/ml.
The protein sample was mixed with Trypsin at a 1:1000 (W/W) Trypsin:protein ratio before setting up crystallization.
Crystal was initially obtained from Molecular Dimentions Proplex screen condition E04.
Crystal used for structure refinement was grown in 20% PEG8000, 10% Glycerol, 0.1M HEPES pH 7.0 in hanging drop setup, using 1.5uL protein, 1.5uL well solution over 0.5 mL reservoir buffer at 20 C.
Crystals grow to mountable size in 4 days. Harvested crystal was flash-frozen in liquid nitrogen. 20% Glycerol was used as the cryo-protectant
Crystal Properties Matthews coefficient Solvent content 3 58.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.867 α = 90 b = 139.867 β = 90 c = 59.386 γ = 120
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 315 ADSC Q315 2013-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3 50 100 0.071 0.074 0.028 8.7 7.6 26035
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.05 100 0.979 0.37 0.754 7.8 1286
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 2ZNV 3 50.01 25473 549 99.97 0.2283 0.22724 0.2267 0.27659 0.2677 RANDOM 96.238
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] -0.73 -0.37 -0.73 2.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.145 r_dihedral_angle_3_deg 14.784 r_dihedral_angle_4_deg 14.769 r_long_range_B_refined 8.905 r_long_range_B_other 8.905 r_mcangle_it 6.248 r_mcangle_other 6.248 r_dihedral_angle_1_deg 6.229 r_scangle_other 5.916 r_mcbond_it 3.933
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.145 r_dihedral_angle_3_deg 14.784 r_dihedral_angle_4_deg 14.769 r_long_range_B_refined 8.905 r_long_range_B_other 8.905 r_mcangle_it 6.248 r_mcangle_other 6.248 r_dihedral_angle_1_deg 6.229 r_scangle_other 5.916 r_mcbond_it 3.933 r_mcbond_other 3.933 r_scbond_it 3.606 r_scbond_other 3.606 r_angle_refined_deg 1.116 r_angle_other_deg 0.937 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7127 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PDB_EXTRACT data extraction MOLREP phasing PHASER phasing