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The crystal structure of the GST-like domains complex of AIMP3-EPRS mutant C92SC105SC123S
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BVX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.4 293.15 Ammonium sulfate, Sodium chloride, Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.94 58.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.063 α = 90 b = 92.063 β = 90 c = 185.948 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 ADSC QUANTUM 315r 2014-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.9796 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.6 50 100 0.157 16.5 5.4 53953 -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 2.6 2.69 100 2.8 5
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 4BVX 2.6 48.93 51915 1980 99.78 0.13917 0.13801 0.1463 0.16957 0.1739 RANDOM 31.298
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] 0.07 0.07 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.531 r_dihedral_angle_4_deg 23.609 r_dihedral_angle_3_deg 18.165 r_dihedral_angle_1_deg 7.734 r_long_range_B_refined 4.998 r_long_range_B_other 4.998 r_mcangle_it 3.442 r_mcangle_other 3.442 r_scangle_other 2.218 r_mcbond_it 2.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.531 r_dihedral_angle_4_deg 23.609 r_dihedral_angle_3_deg 18.165 r_dihedral_angle_1_deg 7.734 r_long_range_B_refined 4.998 r_long_range_B_other 4.998 r_mcangle_it 3.442 r_mcangle_other 3.442 r_scangle_other 2.218 r_mcbond_it 2.015 r_mcbond_other 2.013 r_angle_refined_deg 1.538 r_scbond_it 1.313 r_scbond_other 1.313 r_angle_other_deg 1.049 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 10457 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling Coot model building