☰ Navigation Tabs
Crystal structure of the S18Y variant of ubiquitin carboxy terminal hydrolase L1 bound to ubiquitin vinylmethylester.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ETL PDB ENTRY 2ETL PDB ENTRY 1XD3, CHAIN B experimental model PDB 1XD3 PDB ENTRY 2ETL PDB ENTRY 1XD3, CHAIN B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 298 2.4 M ammonium sulfate, 0.1M BICINE, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.1 41.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.304 α = 90 b = 87.304 β = 90 c = 193.544 γ = 120
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 MARMOSAIC 300 mm CCD mirrors 2009-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0032 APS 23-ID-D
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 2.4 50 98.5 0.094 0.094 21 9.9 11248 11248 2 2
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) 2.4 2.44 99.8 0.6 0.6 3 6.4
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 2ETL
PDB ENTRY 1XD3, CHAIN B 2.4 50 11248 10699 539 98.17 0.21105 0.2089 0.2074 0.25627 0.2565 RANDOM 79.609
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] 0.04 0.02 0.04 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.933 r_dihedral_angle_3_deg 15.346 r_dihedral_angle_4_deg 12.056 r_dihedral_angle_1_deg 4.923 r_angle_refined_deg 0.896 r_scangle_it 0.762 r_scbond_it 0.507 r_nbtor_refined 0.291 r_mcangle_it 0.282 r_symmetry_vdw_refined 0.186
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.933 r_dihedral_angle_3_deg 15.346 r_dihedral_angle_4_deg 12.056 r_dihedral_angle_1_deg 4.923 r_angle_refined_deg 0.896 r_scangle_it 0.762 r_scbond_it 0.507 r_nbtor_refined 0.291 r_mcangle_it 0.282 r_symmetry_vdw_refined 0.186 r_nbd_refined 0.172 r_mcbond_it 0.162 r_xyhbond_nbd_refined 0.097 r_symmetry_hbond_refined 0.087 r_chiral_restr 0.054 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 2344 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 8
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling