☰ Navigation Tabs
Crystal structure of T. cruzi Histidyl-tRNA synthetase in complex with (2-bromophenyl)methanol (Chem 145)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LC0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.2 M ammonium sulfate, 23 % to 28 % PEG 3350, 0.1 M sodium citrate pH 4.8 to 5.3, 1 mM TCEP
Crystal Properties Matthews coefficient Solvent content 2.43 49.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.849 α = 90 b = 118.609 β = 91.32 c = 93.516 γ = 90
Symmetry Space Group C 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 RIGAKU SATURN 944 2013-01-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 2.25 33.23 99 0.113 0.086 0.993 8.6 2.5 45938
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.32 99.5 0.563 0.435 0.669 1.9 2.4 4261
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 3LC0 2.25 32.76 43599 2336 98.89 0.2012 0.1998 0.2026 0.2261 0.228 RANDOM 31.773
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] -0.91 0.06 1.17 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.037 r_dihedral_angle_4_deg 16.025 r_dihedral_angle_3_deg 13.529 r_dihedral_angle_1_deg 5.391 r_angle_refined_deg 1.141 r_mcangle_it 0.873 r_angle_other_deg 0.797 r_mcbond_it 0.495 r_mcbond_other 0.494 r_chiral_restr 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.037 r_dihedral_angle_4_deg 16.025 r_dihedral_angle_3_deg 13.529 r_dihedral_angle_1_deg 5.391 r_angle_refined_deg 1.141 r_mcangle_it 0.873 r_angle_other_deg 0.797 r_mcbond_it 0.495 r_mcbond_other 0.494 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6412 Nucleic Acid Atoms Solvent Atoms 336 Heterogen Atoms 119
Software Software Software Name Purpose DENZO data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing