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Structure of p-boronophenylalanyl tRNA synthetase - apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5N5U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 16 % (w/v) PEG 4000, 0.2 M MgCl2, 0.1 M Tris/HCl
Crystal Properties Matthews coefficient Solvent content 2.48 50.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.001 α = 90 b = 94.008 β = 90.02 c = 286.566 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 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 2.3 34.91 99.9 0.196 0.213 0.99 8.99 6.808 124992 -3 34.372
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 2.3 2.4 100 0.935 1.012 0.602 2.03 6.865
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 5n5u 2.3 34.91 118944 6047 99.9 0.2138 0.2123 0.2146 0.2441 0.2461 RANDOM 33.229
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] -28.78 -0.69 -2.36 31.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.211 r_dihedral_angle_4_deg 16.781 r_dihedral_angle_3_deg 16.12 r_dihedral_angle_1_deg 6.071 r_angle_refined_deg 1.705 r_angle_other_deg 0.983 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.211 r_dihedral_angle_4_deg 16.781 r_dihedral_angle_3_deg 16.12 r_dihedral_angle_1_deg 6.071 r_angle_refined_deg 1.705 r_angle_other_deg 0.983 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19733 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 5
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing