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Crystal structure of alanyl-tRNA synthetase in complex with ATP and L-alanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HY1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 295 16% PEG 3350, 2% v/v TacsimateTM pH5.0, 100 mM sodium citrate tribasic dihydrate pH5.0
Crystal Properties Matthews coefficient Solvent content 2.74 55.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.23 α = 90 b = 55.59 β = 102.072 c = 125.72 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER X 9M 2022-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1.0 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.9 50 99.94 0.999 14.3 6.9 83655 27.9556578494
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.9679 0.102
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.9000034846 29.8003420696 1.34763284735 83638 1998 99.9211507216 0.200286693166 0.199571653002 0.1995 0.230276062234 0.2306 30.1820074522
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.8513741575 f_angle_d 0.943386756438 f_chiral_restr 0.0563125177729 f_bond_d 0.00772009286857 f_plane_restr 0.00573578561309
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6694 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 165
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing