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Crystal structure of deSUMOylase(DUF862)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EBQ PDB ENTRY 3EBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 20% (W/V) POLYETHYLENEGLYCOL 3350 AND 200 MM POTASSIUM PHOSPHATE (PH 5.6)
Crystal Properties Matthews coefficient Solvent content 1.92 36.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.033 α = 90 b = 42.033 β = 90 c = 164.514 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 295 CCD 2008-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A PAL/PLS 4A
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 1.9 30 92.2 0.06 33.01 7.9 11515 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 80 3.4 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3EBQ 1.9 20 1 11499 596 92.5 0.2234 0.2234 0.2108 0.2282 RANDOM
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] 1.639 1.639 -3.277
RMS Deviations Key Refinement Restraint Deviation c_angle_deg 1.33148 c_bond_d 0.005778 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d
RMS Deviations Key Refinement Restraint Deviation c_angle_deg 1.33148 c_bond_d 0.005778 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1225 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing