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Crystal structure of the C2 Domain of the E3 Ubiquitin-Protein Ligase NEDD4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NSQ PDB entry 2NSQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 10% PEG 4000, 0.1 M Succinic acid pH 7.0, 0.01M Spermine tetra-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.21 44.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.778 α = 108.89 b = 47.997 β = 111.11 c = 50.786 γ = 100.86
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2007-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.8 30 95 0.046 28.51 4.1 26613 26613 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.86 79.1 0.364 3 3.7 2230
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2NSQ 1.8 27.23 26612 25255 1357 94.78 0.17056 0.16852 0.1699 0.2086 0.207 RANDOM 30.718
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 -0.4 0.41 -1.26 -0.49 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.155 r_dihedral_angle_4_deg 15.397 r_dihedral_angle_3_deg 14.661 r_dihedral_angle_1_deg 6.818 r_scangle_it 4.852 r_scbond_it 3.418 r_mcangle_it 2.383 r_mcbond_it 1.767 r_angle_refined_deg 1.456 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.155 r_dihedral_angle_4_deg 15.397 r_dihedral_angle_3_deg 14.661 r_dihedral_angle_1_deg 6.818 r_scangle_it 4.852 r_scbond_it 3.418 r_mcangle_it 2.383 r_mcbond_it 1.767 r_angle_refined_deg 1.456 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.242 r_nbd_refined 0.201 r_symmetry_hbond_refined 0.183 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.118 r_metal_ion_refined 0.115 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2330 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing