☰ Navigation Tabs
Crystal structure of human Otubain 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TFF PDB entry 1TFF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 30% PEG 8000, 0.2 M Sodium acetate, 0.1 M Sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.04 39.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.25 α = 90 b = 50.886 β = 101.96 c = 54.722 γ = 90
Symmetry Space Group C 1 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 IMAGE PLATE RIGAKU RAXIS IV 2007-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT
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 1.69 35 97.2 18.7 3.1 23651
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 PDB entry 1TFF 1.69 29.15 22222 1193 95.93 0.19466 0.19223 0.1915 0.23891 0.2334 RANDOM 29.297
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] -0.2 0.59 0.05 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.702 r_dihedral_angle_4_deg 17.906 r_dihedral_angle_3_deg 13.413 r_dihedral_angle_1_deg 5.91 r_scangle_it 5.322 r_scbond_it 4.714 r_mcangle_it 2.603 r_mcbond_it 1.911 r_angle_refined_deg 1.435 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.702 r_dihedral_angle_4_deg 17.906 r_dihedral_angle_3_deg 13.413 r_dihedral_angle_1_deg 5.91 r_scangle_it 5.322 r_scbond_it 4.714 r_mcangle_it 2.603 r_mcbond_it 1.911 r_angle_refined_deg 1.435 r_nbtor_refined 0.305 r_xyhbond_nbd_refined 0.281 r_symmetry_vdw_refined 0.255 r_nbd_refined 0.212 r_symmetry_hbond_refined 0.116 r_chiral_restr 0.093 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 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 1842 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing