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Crystal structure of a LonA protease domain in complex with bortezomib
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 6.5 295 0.2 M sodium citrate pH 6.5 and 10 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.39 63.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.343 α = 90 b = 122.343 β = 90 c = 103.125 γ = 120
Symmetry Space Group P 6 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 CCD RAYONIX MX325HE 2014-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 0.8 NSRRC BL15A1
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 1.85 20 100 0.11 33.44 21.7 39226 39225 2
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 1.85 1.92 100 4.629
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.85 19.85 37301 1924 99.8 0.17835 0.17714 0.1879 0.20094 0.2064 RANDOM 22.072
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] -0.1 -0.05 -0.1 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.246 r_dihedral_angle_4_deg 19.296 r_dihedral_angle_3_deg 13.703 r_long_range_B_refined 5.468 r_dihedral_angle_1_deg 5.279 r_long_range_B_other 5.109 r_scangle_other 3.256 r_scbond_it 2.021 r_scbond_other 2.014 r_mcangle_other 2.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.246 r_dihedral_angle_4_deg 19.296 r_dihedral_angle_3_deg 13.703 r_long_range_B_refined 5.468 r_dihedral_angle_1_deg 5.279 r_long_range_B_other 5.109 r_scangle_other 3.256 r_scbond_it 2.021 r_scbond_other 2.014 r_mcangle_other 2.013 r_mcangle_it 2.012 r_angle_refined_deg 1.386 r_mcbond_it 1.265 r_mcbond_other 1.26 r_angle_other_deg 0.805 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2213 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing HKL-2000 data scaling Coot model building