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Structure of ubiquitin solved by SAD using the Lanthanide-Binding Tag
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 298 0.1M HEPES pH 7.5, 3.7 M NaCl, 33% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50
Crystal Properties Matthews coefficient Solvent content 4.48 72.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.87 α = 90 b = 57.87 β = 90 c = 115.26 γ = 120
Symmetry Space Group P 32 2 1
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 315 SI-111 MONO, MIRRORS 2005-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.6 50 98.4 0.127 15.8 8.5 7214
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.6 2.69 87.7 0.378 2.8 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.6 30.49 6147 6147 285 100 0.218 0.216 0.2104 0.254 0.2603 RANDOM 48.73
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] 6 3 6 -8.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.403 r_dihedral_angle_3_deg 19.897 r_dihedral_angle_4_deg 10.225 r_dihedral_angle_1_deg 7.514 r_scangle_it 2.171 r_angle_other_deg 1.959 r_angle_refined_deg 1.608 r_scbond_it 1.389 r_mcangle_it 0.908 r_mcbond_it 0.766
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.403 r_dihedral_angle_3_deg 19.897 r_dihedral_angle_4_deg 10.225 r_dihedral_angle_1_deg 7.514 r_scangle_it 2.171 r_angle_other_deg 1.959 r_angle_refined_deg 1.608 r_scbond_it 1.389 r_mcangle_it 0.908 r_mcbond_it 0.766 r_symmetry_hbond_refined 0.32 r_nbd_refined 0.286 r_symmetry_vdw_refined 0.27 r_symmetry_vdw_other 0.267 r_xyhbond_nbd_refined 0.258 r_nbd_other 0.238 r_nbtor_refined 0.196 r_chiral_restr 0.18 r_metal_ion_refined 0.121 r_nbtor_other 0.11 r_mcbond_other 0.085 r_bond_refined_d 0.013 r_bond_other_d 0.008 r_gen_planes_refined 0.003 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 871 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 2
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SnB phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction