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PET hydrolase PET6 from halophilic organsim Vibrio gazogenes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XJH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 293 Buffer for protein (150mM NaCl, 25mM HEPES, pH 7.4), protein concentration 12.3 mg/ml;
1:1 drops 0.4 microliter each
Condition:
0.1M Sodium/Potassiumphosphate
35% MPD
No cryo
Crystal Properties Matthews coefficient Solvent content 2.1 41.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.82 α = 119.779 b = 72.61 β = 91.64 c = 72.76 γ = 91.824
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 PILATUS3 S 2M 2020-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
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 1.4 25.7 95.77 0.04679 0.05424 0.0271 0.999 19.45 3.8 150015 9.53
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 1.4 1.45 91.87 0.2477 0.3 0.1654 0.928 4.7 2.6
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 5xjh 1.4 25.7 1.98 149941 7494 95.76 0.1009 0.0996 0.0996 0.1264 0.1266 15.68
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 18.3027 f_angle_d 1.5153 f_chiral_restr 0.1219 f_bond_d 0.0143 f_plane_restr 0.0116
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6456 Nucleic Acid Atoms Solvent Atoms 960 Heterogen Atoms 174
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing