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1.9 Angstrom resolution crystal structure of uncharacterized protein lmo2446 from Listeria monocytogenes EGD-e in complex with alpha-D-glucose, beta-D-glucose, magnesium and calcium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KMQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 295 crystallization conditions - 0.2 M magnesium formate, 20% (w/v) PEG3350 (The JCSG+ suite: A5), protein - 7.3 mg/mL in 10 mM Tris-HCl pH8.3 500 mM NaCl 5 mM BME, soak/cryo - crystallization conditions + 50% glucose, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.53 51.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.125 α = 90 b = 102.962 β = 104.93 c = 75.006 γ = 90
Symmetry Space Group C 1 2 1
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 MARMOSAIC 300 mm CCD Mirror 2013-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.0782 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 30 98.5 0.076 15.8 3.6 94351 94351 -3 22.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 97.5 0.568 2.6 3.6 4671
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 4KMQ 1.9 29.92 89621 89621 4730 98.36 0.13686 0.13508 0.1456 0.17075 0.1782 RANDOM 20.468
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] 0.43 1.82 0.2 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.062 r_dihedral_angle_4_deg 15.047 r_dihedral_angle_3_deg 10.189 r_dihedral_angle_1_deg 4.417 r_scangle_it 3.589 r_scbond_it 2.335 r_angle_refined_deg 1.573 r_mcangle_it 1.294 r_angle_other_deg 0.872 r_mcbond_it 0.729
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.062 r_dihedral_angle_4_deg 15.047 r_dihedral_angle_3_deg 10.189 r_dihedral_angle_1_deg 4.417 r_scangle_it 3.589 r_scbond_it 2.335 r_angle_refined_deg 1.573 r_mcangle_it 1.294 r_angle_other_deg 0.872 r_mcbond_it 0.729 r_mcbond_other 0.231 r_chiral_restr 0.096 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8335 Nucleic Acid Atoms Solvent Atoms 1232 Heterogen Atoms 129
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling