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Crystal structure of a hexameric LonA protease bound to three ADPs
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YPN 4YPN, 1QZM and 1RR9 experimental model PDB 1QZM 4YPN, 1QZM and 1RR9 experimental model PDB 1RR9 4YPN, 1QZM and 1RR9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 8.7 295 0.1 M Tris-HCl pH 8.7, 0.1 M CaCl2, 10-13% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.63 53.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.044 α = 90 b = 169.128 β = 90 c = 135.361 γ = 90
Symmetry Space Group P 21 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 200 CCD RAYONIX MX300HE 2014-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.45 50 99.5 0.168 5.6 52050 45968 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 3.45 3.47 99.6 2.53 5.4
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 4YPN, 1QZM and 1RR9 3.45 30 45968 2447 93.47 0.23859 0.2372 0.237 0.2648 0.262 RANDOM 66.574
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] -1.38 1 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.025 r_dihedral_angle_3_deg 22.447 r_dihedral_angle_4_deg 19.299 r_dihedral_angle_1_deg 7.984 r_long_range_B_refined 7.788 r_long_range_B_other 7.788 r_mcangle_it 4.656 r_mcangle_other 4.656 r_scangle_other 4.025 r_angle_other_deg 3.543
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.025 r_dihedral_angle_3_deg 22.447 r_dihedral_angle_4_deg 19.299 r_dihedral_angle_1_deg 7.984 r_long_range_B_refined 7.788 r_long_range_B_other 7.788 r_mcangle_it 4.656 r_mcangle_other 4.656 r_scangle_other 4.025 r_angle_other_deg 3.543 r_mcbond_it 2.737 r_mcbond_other 2.737 r_scbond_it 2.244 r_scbond_other 2.244 r_angle_refined_deg 1.517 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 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 25091 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 267
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing HKL-2000 data scaling