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Crystal structure of human AMSH-LP DUB domain in complex with Lys63-linked ubiquitin dimer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZNR PDB ENTRIES 2ZNR and 1ubq experimental model PDB 1UBQ PDB ENTRIES 2ZNR and 1ubq
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 180mM tri-ammonium citrate (pH 7.0), 24% PEG 3350, 3% 1,6-Hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.17 43.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.089 α = 90 b = 97.363 β = 97.49 c = 87.894 γ = 90
Symmetry Space Group P 1 21 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 210 mirrors 2008-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.00000 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 1.6 87.04 97.3 0.068 16.9 83683 83683 -0.5
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) 1.6 1.62 90.7 0.267 3.2
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 ENTRIES 2ZNR and 1ubq 1.6 32.47 83683 77359 4051 97.15 0.18511 0.1835 0.183 0.21522 0.2148 RANDOM 15.093
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] -0.25 0.15 0.02 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.822 r_dihedral_angle_4_deg 17.307 r_dihedral_angle_3_deg 12.863 r_dihedral_angle_1_deg 5.747 r_scangle_it 3.724 r_scbond_it 2.248 r_mcangle_it 1.48 r_angle_refined_deg 1.265 r_mcbond_it 0.858 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.822 r_dihedral_angle_4_deg 17.307 r_dihedral_angle_3_deg 12.863 r_dihedral_angle_1_deg 5.747 r_scangle_it 3.724 r_scbond_it 2.248 r_mcangle_it 1.48 r_angle_refined_deg 1.265 r_mcbond_it 0.858 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.218 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.178 r_symmetry_hbond_refined 0.14 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 5072 Nucleic Acid Atoms Solvent Atoms 605 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing