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PylRS C-terminus domain mutant bound with D-3-bromophenylalanine and AMPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZCE 2ZCE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 100 mM HEPES buffer pH 7.5, 10% PEG 8000, 10% Ethylene Glycerol
Crystal Properties Matthews coefficient Solvent content 3.58 65.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.198 α = 90 b = 105.198 β = 90 c = 71.694 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD RAYONIX MX300HE 2017-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.75 28.2 100 0.056 0.017 55.5 11.4 45530 24.3372328819
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.81 0.445 0.132 0.962
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2ZCE 1.75050958755 28.1702948531 1.38114917239 45504 2011 99.9802254301 0.172967683239 0.172443704989 0.1739 0.184316416937 0.1841 30.2227081296
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 23.740654366 f_angle_d 1.11895963872 f_chiral_restr 0.0681734680093 f_plane_restr 0.00873296646534 f_bond_d 0.00830288584341
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2111 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 46
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing