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PylRS Y306G, Y384F, I405R mutant in complex with AMP-PNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q7E PDB ENTRY 1Q7E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1 M SODIUM ACETATE, 15% PEG3350
Crystal Properties Matthews coefficient Solvent content 3.37 63.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.742 α = 90 b = 105.742 β = 90 c = 69.674 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 PIXEL DECTRIS PILATUS 2012-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 2.35 45 100 0.06 20.1 8.4 18610 1.5
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 2.35 2.48 100 0.7 3.6 8.6
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 PDB ENTRY 1Q7E 2.35 38.29 17669 914 99.9 0.17594 0.17444 0.1769 0.20372 0.2022 RANDOM 60.881
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] -0.62 -0.62 -0.62 2.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.924 r_dihedral_angle_4_deg 17.336 r_dihedral_angle_3_deg 15.045 r_dihedral_angle_1_deg 6.516 r_mcangle_it 4.102 r_scbond_it 3.978 r_mcbond_it 2.693 r_mcbond_other 2.679 r_angle_refined_deg 1.701 r_angle_other_deg 1.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.924 r_dihedral_angle_4_deg 17.336 r_dihedral_angle_3_deg 15.045 r_dihedral_angle_1_deg 6.516 r_mcangle_it 4.102 r_scbond_it 3.978 r_mcbond_it 2.693 r_mcbond_other 2.679 r_angle_refined_deg 1.701 r_angle_other_deg 1.156 r_chiral_restr 0.164 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2115 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling