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Crystal structure of prolyl-tRNA synthetase from Naegleria fowleri in complex with proline and adenosine monophophsphate (AMP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HVC PDB entry 4hvcAB as per MoRDa
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 Anatrace TOP86 screen, condition D7: 200mM Ammonium sulfate, 30% PEG 8000: NAFOA.18681.a.B2.PW37988 at 22.6mg/ml + 5mM CaCl2: cryo 15% EG: tray 287001 d7: puck XFD3-8
Crystal Properties Matthews coefficient Solvent content 2.41 48.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.93 α = 90 b = 66.1 β = 102.03 c = 112.98 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 RAYONIX MX-300 2018-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 38.372 99.4 0.08 0.094 0.997 12.78 3.671 76263 29.581
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 2.05 94.4 0.495 0.606 0.739 2.24 2.823
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 4hvcAB as per MoRDa 2 38.372 1.35 76253 1991 99.4 0.1522 0.1512 0.1523 0.1916 0.1924 0 29.5298
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.363 f_angle_d 0.843 f_chiral_restr 0.054 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7919 Nucleic Acid Atoms Solvent Atoms 802 Heterogen Atoms 116
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction SIMBAD phasing PHASER phasing ARP/wARP model building Coot model building MoRDa phasing