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Structure of p-boronophenylalanyl tRNA synthetase in complex with p-boronophenylalanine and adenosine monophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NDA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 20 % (w/v) PEG 1000, 0.2 M MgCl2, 0.1 M sodium cacodylate
Crystal Properties Matthews coefficient Solvent content 2.32 47.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.582 α = 90 b = 38.735 β = 90.28 c = 82.034 γ = 90
Symmetry Space Group P 1 2 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 CCD MARMOSAIC 225 mm CCD 2016-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.3 0.8943 BESSY 14.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.6 30 99.7 0.043 0.046 1 24.36 7.43 43906 -3 31.967
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.7 99.5 0.717 0.771 0.909 3.18 7.497
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 4NDA 1.6 30 41806 2100 99.67 0.1777 0.176 0.1856 0.2129 0.2179 RANDOM 33.232
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] -1.09 -1.16 1.97 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.283 r_dihedral_angle_4_deg 16.369 r_dihedral_angle_3_deg 14.23 r_dihedral_angle_1_deg 5.892 r_angle_refined_deg 2.051 r_angle_other_deg 1.055 r_chiral_restr 0.131 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.283 r_dihedral_angle_4_deg 16.369 r_dihedral_angle_3_deg 14.23 r_dihedral_angle_1_deg 5.892 r_angle_refined_deg 2.051 r_angle_other_deg 1.055 r_chiral_restr 0.131 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2473 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 41
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing