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Crystal structure of Zn2-hUb (human ubiquitin) adduct from a solution 35 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, 35 mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.08 40.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.84 α = 90 b = 50.33 β = 90 c = 94.03 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 34.36 99.8 0.242 0.242 5.3 5.8 21412 21381 3 3 20.4
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 99.2 0.327 0.327 4.3 5.9 3024
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 34.36 20239 20239 1095 99.71 0.2125 0.2125 0.20943 0.2112 0.27104 0.2707 RANDOM 12.019
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] -0.03 0.28 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.064 r_dihedral_angle_4_deg 17.609 r_dihedral_angle_3_deg 16.821 r_dihedral_angle_1_deg 5.714 r_scangle_it 5.358 r_scbond_it 3.345 r_angle_refined_deg 1.969 r_mcangle_it 1.861 r_mcbond_it 1.154 r_chiral_restr 0.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.064 r_dihedral_angle_4_deg 17.609 r_dihedral_angle_3_deg 16.821 r_dihedral_angle_1_deg 5.714 r_scangle_it 5.358 r_scbond_it 3.345 r_angle_refined_deg 1.969 r_mcangle_it 1.861 r_mcbond_it 1.154 r_chiral_restr 0.138 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1703 Nucleic Acid Atoms Solvent Atoms 352 Heterogen Atoms 22
Software Software Software Name Purpose AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling