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Structure of the HAD domain of effector protein Lem4 (lpg1101) from Legionella pneumophila (inactive mutant)with phosphate bound in the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CGJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M Bis-Tris 6.5, 22% PEG 3350, 0.2 M Mg acetate, 0.6 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.05 39.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.627 α = 90 b = 105.627 β = 90 c = 36.255 γ = 90
Symmetry Space Group P 4 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 CCD RAYONIX MX225HE 2017-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
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 1.668 52.814 100 0.087 0.09 0.024 0.999 19.7 14.3 24546 22.2
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 1.668 1.674 97.1 1.359 1.408 0.367 0.915 14.4
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 6CGJ 1.668 47.238 1.34 24476 1199 99.76 0.1901 0.1883 0.189 0.2264 0.2291 40.5311
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1551 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 20
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing