☰ Navigation Tabs
Structural Analysis of Xanthomonas XopD Provides Insights Into Substrate Specificity of Ubiquitin-like Protein Proteases
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 15 mg/mL protein in 20 mM Tris-HCl pH 7.5, 75 mM KCl, and 0.5 mM DTT, 1.4 - 1.6 M sodium potassium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.26 45.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.618 α = 90 b = 91.618 β = 90 c = 44.82 γ = 90
Symmetry Space Group P 41 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 100 CCD SBC-3 2004-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97929 APS 19-BM
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 1.95 32.04 98.6 0.061 31.2 7.6 14282 14282 37.8
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 1.95 2 99.9 0.71 2.25 7.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SAD THROUGHOUT 1.95 32.04 14274 13554 720 100 0.21012 0.21012 0.20795 0.212 0.25017 0.2576 RANDOM 42.341
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] -1.33 -1.33 2.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.803 r_dihedral_angle_4_deg 21.515 r_dihedral_angle_3_deg 15.209 r_dihedral_angle_1_deg 6.485 r_scangle_it 3.45 r_scbond_it 2.367 r_mcangle_it 1.642 r_angle_refined_deg 1.48 r_mcbond_it 1.033 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.803 r_dihedral_angle_4_deg 21.515 r_dihedral_angle_3_deg 15.209 r_dihedral_angle_1_deg 6.485 r_scangle_it 3.45 r_scbond_it 2.367 r_mcangle_it 1.642 r_angle_refined_deg 1.48 r_mcbond_it 1.033 r_nbtor_refined 0.303 r_symmetry_hbond_refined 0.251 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.173 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.099 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1350 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing