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Crystal structure of the OTU domain of OTULIN D336A mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZNV PDB ENTRY 3ZNV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 100 MM MES/IMIDAZOLE PH 6.5, 30 MM MGCL2, 30 MM CACL2, 10% PEG 4,000, 20% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.45 49.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.807 α = 90 b = 72.197 β = 90 c = 94.843 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 287 CCD ADSC QUANTUM 315r MIRROR 2012-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.35 47.42 100 0.09 9.9 6.1 66908 3
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 1.35 1.37 100 0.7 2.4 4.7
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 ENTRY 3ZNV 1.35 47.47 63440 3382 99.94 0.12349 0.12163 0.1366 0.15894 0.1659 RANDOM 18.363
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] 0.37 -0.4 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.837 r_dihedral_angle_4_deg 21.292 r_sphericity_bonded 20.514 r_dihedral_angle_3_deg 12.849 r_rigid_bond_restr 10.739 r_scangle_it 6.607 r_scbond_it 5.721 r_dihedral_angle_1_deg 5.628 r_mcangle_it 3.734 r_mcbond_it 3.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.837 r_dihedral_angle_4_deg 21.292 r_sphericity_bonded 20.514 r_dihedral_angle_3_deg 12.849 r_rigid_bond_restr 10.739 r_scangle_it 6.607 r_scbond_it 5.721 r_dihedral_angle_1_deg 5.628 r_mcangle_it 3.734 r_mcbond_it 3.222 r_mcbond_other 3.206 r_angle_refined_deg 1.462 r_angle_other_deg 1 r_symmetry_vdw_refined 0.354 r_xyhbond_nbd_other 0.353 r_nbd_refined 0.347 r_xyhbond_nbd_refined 0.311 r_symmetry_vdw_other 0.228 r_nbd_other 0.222 r_nbtor_refined 0.19 r_chiral_restr 0.102 r_metal_ion_refined 0.097 r_nbtor_other 0.085 r_symmetry_hbond_refined 0.059 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2094 Nucleic Acid Atoms Solvent Atoms 330 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALEPACK data scaling