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Crystal structure of LigU(K66M) bound to substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6P3K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 Well - 1000 mM Sodium citrate tribasic, 100 mM Sodium cacodylate/HCl, pH 6.5
Drop - 100 nL enzyme, 100 nL OMA (5 mM), 500 nL well where the enzyme concentration was 20 mg/mL in 20 mM HEPES/KOH pH 7.9
Crystal Properties Matthews coefficient Solvent content 3.15 60.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.88 α = 90 b = 134 β = 90 c = 168.37 γ = 90
Symmetry Space Group P 21 21 2
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 EIGER X 16M 2019-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 1.1271 SSRL BL14-1
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 1.62 39.53 97.5 0.091 0.101 0.044 0.997 8.8 5.1 236378 20.09
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.62 1.65 94.2 0.597 0.659 0.276 0.446 5.2
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 THROUGHOUT 6P3K 1.62 39.46 1.34 236265 2000 97.21 0.1568 0.1566 0.156 0.1869 0.187 29.43
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 8.9688 f_angle_d 1.3941 f_chiral_restr 0.1018 f_bond_d 0.0166 f_plane_restr 0.0088
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10072 Nucleic Acid Atoms Solvent Atoms 1516 Heterogen Atoms 62
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction