☰ Navigation Tabs
Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase)from Plasmodium falciparum in complex with Halofuginone and AMPPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NCX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 Protein incubated with 4mM each of AMPPnP, halofuginone, B-ME, and MgCl2 for 5min, then added 1 to 1 with Wiz3/4(h5)- 20%PEG-8000, 0.1M HEPES/NaOH, pH=7.5, 10% isopropanol, 0.2M AmSO4, cryoprotected with 20%EG, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 5.17 76.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.55 α = 90 b = 106.55 β = 90 c = 186.16 γ = 120
Symmetry Space Group P 31 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 ADSC QUANTUM 315r 2014-01-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.977408 ALS 5.0.1
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 2.9 50 98.4 0.046 23.56 3.8 27848 27391 -3 68.204
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 2.9 2.98 99 0.558 3.13
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4NCX 2.9 46.237 28694 27357 1337 98.39 0.1994 0.1976 0.2363 0.2195 RANDOM 74.425
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] 0.51 0.25 0.51 -1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.236 r_dihedral_angle_4_deg 17.864 r_dihedral_angle_3_deg 16.301 r_dihedral_angle_1_deg 6.784 r_mcangle_it 3.618 r_mcbond_it 2.295 r_mcbond_other 2.295 r_angle_refined_deg 1.482 r_angle_other_deg 0.786 r_chiral_restr 0.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.236 r_dihedral_angle_4_deg 17.864 r_dihedral_angle_3_deg 16.301 r_dihedral_angle_1_deg 6.784 r_mcangle_it 3.618 r_mcbond_it 2.295 r_mcbond_other 2.295 r_angle_refined_deg 1.482 r_angle_other_deg 0.786 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3773 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 135
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction BOS data collection