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Crystal structure of a LonA fragment containing the 3-helix bundle and the AAA-alpha/beta domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M6A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 5.5 295 0.1 M sodium citrate pH 5.5, 25 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.96 37.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.203 α = 90 b = 63.892 β = 90 c = 69.298 γ = 90
Symmetry Space Group P 21 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 PIXEL DECTRIS PILATUS 2M-F 2013-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.1 Photon Factory BL-1A
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 2.07 50 99.8 0.086 19.49 6.1 16502 15628 2
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 2.07 2.14 100 0.575 4.62 6.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3M6A 2.07 30 15627 833 99.19 0.18747 0.18488 0.23657 0.2568 RANDOM 37.758
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] 0.39 -0.42 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.413 r_dihedral_angle_4_deg 22.701 r_dihedral_angle_3_deg 15.627 r_long_range_B_refined 8.089 r_long_range_B_other 8.022 r_dihedral_angle_1_deg 6.981 r_scangle_other 5.591 r_mcangle_it 4.15 r_mcangle_other 4.149 r_scbond_it 3.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.413 r_dihedral_angle_4_deg 22.701 r_dihedral_angle_3_deg 15.627 r_long_range_B_refined 8.089 r_long_range_B_other 8.022 r_dihedral_angle_1_deg 6.981 r_scangle_other 5.591 r_mcangle_it 4.15 r_mcangle_other 4.149 r_scbond_it 3.56 r_scbond_other 3.559 r_mcbond_it 2.764 r_mcbond_other 2.751 r_angle_refined_deg 1.892 r_angle_other_deg 0.947 r_chiral_restr 0.132 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 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 1985 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing HKL-2000 data scaling