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Structure of a Short-Chain Flavodoxin Associated with a Non-Canonical PDU Bacterial Microcompartment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LJL PDB entry 5LJL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 25% PEG3350, 200 mM calcium acetate, 100 mM MES, pH 5.5, 6 mM cadmium acetate
Crystal Properties Matthews coefficient Solvent content 2 38.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.301 α = 90 b = 95.807 β = 90 c = 102.378 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 PILATUS3 6M 2016-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0004 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.99 48 100 0.091 0.999 16.3 12.4 32751
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.04 100 0.903 0.79 10.3
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 FREE R-VALUE PDB entry 5LJL 1.99 47.904 1.35 32687 2003 99.98 0.2038 0.2007 0.2037 0.2497 0.2512 random selection
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 3.188 f_angle_d 0.804 f_chiral_restr 0.048 f_bond_d 0.007 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3421 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 102
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing