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Crystal Structure of a human cytosolic histidyl-tRNA synthetase, histidine-bound
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.1 M Tris pH 7 to 9, 0.2 M MgCl2 and 20 to 32.5% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.35 47.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.087 α = 90 b = 92.993 β = 90 c = 261.083 γ = 90
Symmetry Space Group P 21 21 21
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 6M 2012-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.98 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.84 39.41 95.3 0.148 0.075 9 4.3 49252
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.84 2.94 89.4 0.983 0.51 1.6 3.9 4201
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.844 39.41 49209 2504 94.69 0.2024 0.2005 0.2039 0.238 0.2361 RANDOM 62.176
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] -0.82 -0.04 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.289 r_dihedral_angle_4_deg 18.512 r_dihedral_angle_3_deg 14.481 r_dihedral_angle_1_deg 5.419 r_mcangle_it 2.517 r_mcbond_it 1.469 r_mcbond_other 1.469 r_angle_refined_deg 1.157 r_angle_other_deg 0.957 r_chiral_restr 0.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.289 r_dihedral_angle_4_deg 18.512 r_dihedral_angle_3_deg 14.481 r_dihedral_angle_1_deg 5.419 r_mcangle_it 2.517 r_mcbond_it 1.469 r_mcbond_other 1.469 r_angle_refined_deg 1.157 r_angle_other_deg 0.957 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_bond_other_d 0.004 r_gen_planes_refined 0.004 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13957 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 68
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing