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SUMO protease Ulp1 with the catalytic cysteine oxidized to a sulfenic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EUV PDB ENTRY 1EUV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 289 20% w/v PEG 3350, 0.2M NaCl and post-soaked in 50mM DTT for 48 hours, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.12 41.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.089 α = 90 b = 40.328 β = 112.02 c = 55.379 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 mirrors 2006-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
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 51.367 99.9 0.084 0.084 5.9 3.1 14736
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 2.11 99.3 0.493 0.493 1.5 3 2117
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1EUV 2.1 51.367 12780 660 99.92 0.218 0.216 0.26 RANDOM 22.401
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] -1.21 -0.69 1.53 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.688 r_dihedral_angle_4_deg 20.382 r_dihedral_angle_3_deg 15.971 r_dihedral_angle_1_deg 5.788 r_scangle_it 4.367 r_scbond_it 3.276 r_mcangle_it 2.164 r_angle_refined_deg 1.97 r_mcbond_it 1.798 r_angle_other_deg 1.189
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.688 r_dihedral_angle_4_deg 20.382 r_dihedral_angle_3_deg 15.971 r_dihedral_angle_1_deg 5.788 r_scangle_it 4.367 r_scbond_it 3.276 r_mcangle_it 2.164 r_angle_refined_deg 1.97 r_mcbond_it 1.798 r_angle_other_deg 1.189 r_symmetry_vdw_other 0.38 r_mcbond_other 0.379 r_symmetry_vdw_refined 0.358 r_xyhbond_nbd_refined 0.215 r_nbd_refined 0.209 r_nbd_other 0.194 r_nbtor_refined 0.176 r_chiral_restr 0.146 r_symmetry_hbond_refined 0.117 r_nbtor_other 0.089 r_bond_refined_d 0.025 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1782 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction MOLREP phasing