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1.55 Angstrom Crystal Structure of the Four Helical Bundle Membrane Localization Domain (4HBM) of the Vibrio vulnificus MARTX Effector Domain DUF5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EBF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 Protein: 13mG/mL, 0.1M Sodium chloride, TRIS-HCl pH 7.0, 6.9 mM Phosphatidylserine (PS); Screen: JCSG+ (G10), 0.15M Potassium bromide, 30% w/v PEG MME 2000, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.99 38.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.896 α = 90 b = 49.874 β = 90 c = 72.102 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 CCD MARMOSAIC 300 mm CCD Beryllium lenses 2012-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 1.55 30 99.6 0.054 26.7 6 24039 24039 -3 28.7
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 1.55 1.58 99.4 0.555 3.1 5.3 1175
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 (All) 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 2EBF 1.55 29.22 22766 22766 1223 99.38 0.16983 0.16983 0.16717 0.1714 0.2152 0.21 RANDOM 23.373
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] -0.5 1.19 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.114 r_dihedral_angle_3_deg 13.26 r_dihedral_angle_4_deg 10.595 r_scangle_it 6.532 r_scbond_it 4.42 r_dihedral_angle_1_deg 3.671 r_mcangle_it 3.268 r_mcbond_it 1.97 r_angle_refined_deg 1.187 r_rigid_bond_restr 1.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.114 r_dihedral_angle_3_deg 13.26 r_dihedral_angle_4_deg 10.595 r_scangle_it 6.532 r_scbond_it 4.42 r_dihedral_angle_1_deg 3.671 r_mcangle_it 3.268 r_mcbond_it 1.97 r_angle_refined_deg 1.187 r_rigid_bond_restr 1.063 r_angle_other_deg 0.852 r_mcbond_other 0.828 r_chiral_restr 0.075 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1285 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 4
Software Software Software Name Purpose Blu-Ice data collection PHENIX model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing