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yeast Deubiquitinase Ubp3 and Bre5 cofactor complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZX2 PDB 1ZX2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 9 293 10%(w/v) PEG 20000, 100mM Bicine, 2% Dioxan, pH 9.0, EVAPORATION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.95 58.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.1 α = 90 b = 90.24 β = 90 c = 101.48 γ = 90
Symmetry Space Group P 21 21 21
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 4 2006-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.9176 CHESS F1
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 49.45 3.9 59376 50599
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 1.69 1.75 0.371 3.2
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 1ZX2 1.69 49.45 50599 5681 94.83 0.2084 0.20659 0.207 0.22458 0.2244 RANDOM 29.552
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] 0.77 -1.59 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.286 r_dihedral_angle_4_deg 19.12 r_dihedral_angle_3_deg 15.438 r_dihedral_angle_1_deg 5.661 r_scangle_it 3.246 r_scbond_it 2.241 r_angle_refined_deg 1.469 r_mcangle_it 1.402 r_mcbond_it 0.87 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.286 r_dihedral_angle_4_deg 19.12 r_dihedral_angle_3_deg 15.438 r_dihedral_angle_1_deg 5.661 r_scangle_it 3.246 r_scbond_it 2.241 r_angle_refined_deg 1.469 r_mcangle_it 1.402 r_mcbond_it 0.87 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.235 r_symmetry_hbond_refined 0.235 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.118 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2580 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing