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X-ray structure of human ubiquitin Cd(II) adduct
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 200mM cadmium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.83 56.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.253 α = 90 b = 105.253 β = 90 c = 105.253 γ = 90
Symmetry Space Group P 43 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 mirrors 2006-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3
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 3 74.43 100 0.084 0.078 76.5 80 4357 2 2 73.8
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) 3 3.1 100 0.7 10 50 242
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 1UBQ 3 74.43 4331 231 99.9 0.279 0.279 0.2747 0.3 0.2914 RANDOM 73.5
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]
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.8 c_improper_angle_d 2.33 c_scangle_it 2.3 c_mcangle_it 2.04 c_angle_deg 1.9 c_scbond_it 1.38 c_mcbond_it 1.12 c_bond_d 0.012 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.8 c_improper_angle_d 2.33 c_scangle_it 2.3 c_mcangle_it 2.04 c_angle_deg 1.9 c_scbond_it 1.38 c_mcbond_it 1.12 c_bond_d 0.012 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1164 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 12
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing CNS refinement DENZO data reduction SCALEPACK data scaling