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Crystal structure of Zn3-hUb(human ubiquitin) adduct from a solution 100 mM zinc acetate/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 7 293 25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 100 mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.02 39.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.88 α = 90 b = 50.51 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 mirrors 2012-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.26 ELETTRA 5.2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.76 34.4 97.7 0.176 0.176 6.3 5.8 21073 20920 3 3 20.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.85 95 0.268 0.268 4.2 5.8 2888
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 (All) 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 1.76 34.4 19689 19689 1071 96.68 0.20312 0.20312 0.19977 0.2042 0.26691 0.2675 RANDOM 13.78
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 0.26 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.156 r_dihedral_angle_4_deg 22.68 r_dihedral_angle_3_deg 15.413 r_dihedral_angle_1_deg 6.12 r_scangle_it 5.776 r_scbond_it 3.587 r_mcangle_it 2.065 r_angle_refined_deg 2.047 r_mcbond_it 1.257 r_chiral_restr 0.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.156 r_dihedral_angle_4_deg 22.68 r_dihedral_angle_3_deg 15.413 r_dihedral_angle_1_deg 6.12 r_scangle_it 5.776 r_scbond_it 3.587 r_mcangle_it 2.065 r_angle_refined_deg 2.047 r_mcbond_it 1.257 r_chiral_restr 0.143 r_bond_refined_d 0.023 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1722 Nucleic Acid Atoms Solvent Atoms 331 Heterogen Atoms 25
Software Software Software Name Purpose AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling