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Crystal structure of Mycobacterium tuberculosis phosphatidylinositol phosphate synthase (PgsA1) in complex with manganese and citrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6H53
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 6 295 31% PEG 400 (v/v), 0.1 M NaCl, 0.12 M MnCl2 and 0.1 M trisodium citrate dihydrate pH 6
Crystal Properties Matthews coefficient Solvent content 2.78 55.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.067 α = 90 b = 77.941 β = 90 c = 100.823 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 EIGER X 16M 2016-05-29 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2016-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00 SLS X06SA 2 SYNCHROTRON SLS BEAMLINE X06SA 1.88 SLS X06SA
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 1.88 45.699 98.87 0.1427 0.1546 0.0587 0.999 9.52 6.8 43956 24.91
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 1.88 1.95 97.92 1.063 1.152 0.439 0.409 1.46 12.8
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6H53 1.88 45.699 1.37 43956 2198 98.87 0.2051 0.2037 0.2047 0.2299 0.2316 Random selection 30.44
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 24.397 f_angle_d 1.268 f_chiral_restr 0.051 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3140 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 428
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHENIX phasing