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Crystal structure of Zn2.3-hUb (human ubiquitin) adduct from a solution 70 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, 70 mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.01 38.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.82 α = 90 b = 50.39 β = 90 c = 93.62 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 34.3 99.4 0.053 0.053 17.1 5.1 21361 21184 3 3 22.4
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 99.8 0.097 0.097 11.4 5.8 3045
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 34.3 20021 20021 1087 99 0.16299 0.16299 0.16117 0.1665 0.19639 0.1992 RANDOM 15.464
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] -0.45 0.38 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.459 r_dihedral_angle_4_deg 22.62 r_dihedral_angle_3_deg 14.38 r_scangle_it 7.155 r_dihedral_angle_1_deg 6.37 r_scbond_it 4.283 r_mcangle_it 2.618 r_angle_refined_deg 2.241 r_mcbond_it 1.535 r_chiral_restr 0.233
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.459 r_dihedral_angle_4_deg 22.62 r_dihedral_angle_3_deg 14.38 r_scangle_it 7.155 r_dihedral_angle_1_deg 6.37 r_scbond_it 4.283 r_mcangle_it 2.618 r_angle_refined_deg 2.241 r_mcbond_it 1.535 r_chiral_restr 0.233 r_bond_refined_d 0.027 r_gen_planes_refined 0.011 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 1722 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 44
Software Software Software Name Purpose AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling