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Crystal structure of Zn3-hUb(human ubiquitin) adduct from a solution 70 mM zinc acetate/20% v/v TFE/1.3 mM hUb
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EHV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 22-30% (w/v) PEG 1450, 50 mM HEPES pH 6.5-7.0, 70 mM Zn(CH3COO)2 and 20% v/v TFE
Crystal Properties Matthews coefficient Solvent content 2 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.79 α = 90 b = 50.32 β = 90 c = 93.95 γ = 90
Symmetry Space Group P 21 21 21
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 2M 2011-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.265 ELETTRA 5.2R
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 1.7 27.02 99.8 0.243 4.4 5.2 23500 3 -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 1.7 1.73 99.8 0.693 1.6 4.3
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 3EHV 1.7 27.02 22311 1136 99.66 0.22728 0.22477 0.2352 0.27639 0.2798 RANDOM 19.027
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] -2.03 1.72 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.676 r_dihedral_angle_4_deg 23.772 r_dihedral_angle_3_deg 16.722 r_dihedral_angle_1_deg 6.926 r_long_range_B_refined 5.81 r_long_range_B_other 5.666 r_scangle_other 3.54 r_mcangle_it 2.516 r_mcangle_other 2.515 r_scbond_it 2.283
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.676 r_dihedral_angle_4_deg 23.772 r_dihedral_angle_3_deg 16.722 r_dihedral_angle_1_deg 6.926 r_long_range_B_refined 5.81 r_long_range_B_other 5.666 r_scangle_other 3.54 r_mcangle_it 2.516 r_mcangle_other 2.515 r_scbond_it 2.283 r_scbond_other 2.282 r_angle_refined_deg 2.087 r_mcbond_it 1.663 r_mcbond_other 1.63 r_angle_other_deg 1.144 r_chiral_restr 0.121 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 1750 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing