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Crystal structure of the I93M mutant 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 3IFW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 298 0.1M BICINE, 2.4M Ammonium Sulfate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.09 41.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.089 α = 90 b = 87.089 β = 90 c = 193.476 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 2009-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 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 2.8 70.2 96.7 0.089 0.089 21.7 10.5 6996 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) 2.8 2.85 99.4 0.856 0.856 2.1 8.4
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 3IFW 2.8 40.72 6666 330 96.7 0.2442 0.24235 0.2382 0.28407 0.2964 RANDOM 109.927
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] -1.91 -0.95 -1.91 2.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.31 r_dihedral_angle_3_deg 15.289 r_dihedral_angle_4_deg 14.994 r_dihedral_angle_1_deg 4.594 r_angle_refined_deg 0.888 r_scangle_it 0.592 r_scbond_it 0.419 r_nbtor_refined 0.29 r_mcangle_it 0.239 r_symmetry_vdw_refined 0.211
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.31 r_dihedral_angle_3_deg 15.289 r_dihedral_angle_4_deg 14.994 r_dihedral_angle_1_deg 4.594 r_angle_refined_deg 0.888 r_scangle_it 0.592 r_scbond_it 0.419 r_nbtor_refined 0.29 r_mcangle_it 0.239 r_symmetry_vdw_refined 0.211 r_nbd_refined 0.172 r_mcbond_it 0.137 r_xyhbond_nbd_refined 0.115 r_symmetry_hbond_refined 0.114 r_chiral_restr 0.056 r_bond_refined_d 0.006 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 2338 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 8
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling