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Histidyl-tRNA synthetase from Trypanosoma cruzi (Histidyl-adenylate complex)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HRJ PDB ENTRY 3HRJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 293 0.2 M Lithium Sulfate, 28% PEG 3350, 0.1 M Bis/Tris pH 5.5, 1mM TCEP, 10 mM L-Histidine; subsequent soak against effective concentration 5mM ATP, 5mM MgCl2, vapor diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.03 59.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.36 α = 90 b = 166.987 β = 90 c = 66.021 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2009-04-22 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97923 SSRL BL9-2
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 3.05 50 80.3 0.12 7.746 3 19599 63
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 3.05 3.16 68.7 0.905 2.7 1641
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 3HRJ 3.05 42.56 19569 1022 80.23 0.236 0.232 0.229 0.308 0.2951 RANDOM 29.905
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] -0.93 5.67 -4.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.036 r_dihedral_angle_3_deg 16.497 r_dihedral_angle_4_deg 14.111 r_dihedral_angle_1_deg 6.072 r_scangle_it 1.488 r_angle_refined_deg 1.119 r_scbond_it 0.824 r_angle_other_deg 0.803 r_mcangle_it 0.69 r_mcbond_it 0.363
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.036 r_dihedral_angle_3_deg 16.497 r_dihedral_angle_4_deg 14.111 r_dihedral_angle_1_deg 6.072 r_scangle_it 1.488 r_angle_refined_deg 1.119 r_scbond_it 0.824 r_angle_other_deg 0.803 r_mcangle_it 0.69 r_mcbond_it 0.363 r_chiral_restr 0.056 r_mcbond_other 0.045 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6477 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 67
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling