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Crystal structure of linear diubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UBQ PDB ENTRY 1UBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 289 30% PEG 4000, 0.1M Tris-HCl, 0.1M MgCl2, 30% Dioxane, 30% Isopropanol , pH 7.5, VAPOR DIFFUSION, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.02 39.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.261 α = 91.79 b = 35.314 β = 112.85 c = 35.841 γ = 112.88
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 315r 2009-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.19 32.26 97.42 6959 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.19 2.244
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 (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 PDB ENTRY 1UBQ 2.19 32.26 10720 6485 325 97.42 0.20933 0.20614 0.2137 0.27798 0.2853 RANDOM 36.478
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] 2.08 -2.65 2.66 -3.05 -2.78 0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.683 r_dihedral_angle_3_deg 18.624 r_dihedral_angle_4_deg 16.89 r_dihedral_angle_1_deg 6.76 r_scangle_it 3.458 r_scbond_it 1.997 r_angle_refined_deg 1.509 r_mcangle_it 1.262 r_mcbond_it 0.675 r_chiral_restr 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.683 r_dihedral_angle_3_deg 18.624 r_dihedral_angle_4_deg 16.89 r_dihedral_angle_1_deg 6.76 r_scangle_it 3.458 r_scbond_it 1.997 r_angle_refined_deg 1.509 r_mcangle_it 1.262 r_mcbond_it 0.675 r_chiral_restr 0.11 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1183 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 6
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling