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Crystal structure of the Lon-like protease MtaLonC with D581A mutation in complex with substrate polypeptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FW9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 295 10% isopropanol, 100 mM monosodium phosphate, 100 mM sodium citrate at pH 4.6.
Crystal Properties Matthews coefficient Solvent content 3.27 62.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.742 α = 90 b = 115.742 β = 90 c = 135.998 γ = 120
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 BRUKER SMART 6500 2011-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 1 SPring-8 BL44XU
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 2.25 20 99.2 0.063 23.7 5.2 48531
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 2.25 2.33 98.2 0.592 2.1 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 4FW9 2.25 19.83 41112 2255 88.5 0.155 0.153 0.1523 0.193 0.1822 RANDOM 36.44
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] -0.73 -0.73 1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.199 r_dihedral_angle_4_deg 19.151 r_dihedral_angle_3_deg 17.696 r_dihedral_angle_1_deg 6.683 r_angle_refined_deg 1.454 r_angle_other_deg 0.797 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.199 r_dihedral_angle_4_deg 19.151 r_dihedral_angle_3_deg 17.696 r_dihedral_angle_1_deg 6.683 r_angle_refined_deg 1.454 r_angle_other_deg 0.797 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4542 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing