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Neisseria gonorrhoeae peptidyl-tRNA hydrolase complexed with an XChem hit.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QT4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.95 291 60uL of the reservoir solution (100 mM Bis-Tris Propane pH 5.95, 200 mM Li2SO4 and 30% PEG 3350) was pipetted into the wells. The drop volume was 0.5uL, composed of 200 nL of 13.7 mg/mL gonoccocal Pth, 200 nL reservoir solution and 100 nL seed crystals. The plate was sealed quickly and kept in an incubator at 18C and the single crystals appeared in 2-7 days.
Crystal Properties Matthews coefficient Solvent content 2.66 53.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.44 α = 90 b = 71.51 β = 90 c = 146.99 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2016-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9282 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.83 37.4 92.2 0.072 0.079 0.032 0.998 16.5 6.3 38126 27.96
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 1.83 1.86 100 2.042 0.841 0.669 1.1 6.8
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 4QT4 1.83 37.4 1.33 37583 1916 90.93 0.336 0.3345 0.3465 0.3641 0.3746 38.49
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 5.7197 f_angle_d 0.8816 f_chiral_restr 0.0527 f_plane_restr 0.0071 f_bond_d 0.0056
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2965 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing