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Double sided ubiquitin binding of Hrs-UIM
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, HANGING DROP 9.5 289 PEG400, CHES, pH 9.50, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.24 45.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.244 α = 90 b = 73.244 β = 90 c = 169.636 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 ADSC QUANTUM 210 2003-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1 Photon Factory AR-NW12A
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 1.7 50 99.8 0.051 16.5 14.9 19706 19682
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) 1.7 1.76 100 0.378 8.45 14.7 1931
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 (All) 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 1.7 36.51 19706 19418 992 98.7 0.1989 0.1989 0.197 0.2119 0.228 0.2119 RANDOM 19.47
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] -0.58 -0.29 -0.58 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.594 r_scangle_it 5.455 r_scbond_it 3.145 r_mcangle_it 2.106 r_angle_refined_deg 1.551 r_mcbond_it 1.137 r_angle_other_deg 0.788 r_symmetry_vdw_other 0.303 r_nbd_other 0.245 r_nbd_refined 0.208
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.594 r_scangle_it 5.455 r_scbond_it 3.145 r_mcangle_it 2.106 r_angle_refined_deg 1.551 r_mcbond_it 1.137 r_angle_other_deg 0.788 r_symmetry_vdw_other 0.303 r_nbd_other 0.245 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.143 r_symmetry_vdw_refined 0.135 r_symmetry_hbond_refined 0.133 r_chiral_restr 0.09 r_nbtor_other 0.079 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 1287 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data reduction MOLREP phasing REFMAC refinement HKL-2000 data scaling