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Structure of the extended diarrhea-inducing domain of rotavirus enterotoxigenic protein NSP4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O1K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 1.0M potassium sodium tetra hydrate, 0.1M HEPES, KOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.1 41.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.614 α = 90 b = 180.432 β = 90 c = 48.691 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 IMAGE PLATE MAR scanner 345 mm plate osmic mirror 2006-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.7 37.8 96.2 0.077 14 5847
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 2.7 2.85 96.2 0.439 3.5 833
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 201K 2.7 15 5545 269 94.49 0.25067 0.24769 0.2421 0.31377 0.3128 RANDOM 20.091
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] 0.73 -4.41 3.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.27 r_dihedral_angle_3_deg 25.689 r_dihedral_angle_4_deg 19.414 r_dihedral_angle_1_deg 6.86 r_scangle_it 3.64 r_scbond_it 2.033 r_angle_refined_deg 1.991 r_mcangle_it 1.257 r_mcbond_it 0.701 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.27 r_dihedral_angle_3_deg 25.689 r_dihedral_angle_4_deg 19.414 r_dihedral_angle_1_deg 6.86 r_scangle_it 3.64 r_scbond_it 2.033 r_angle_refined_deg 1.991 r_mcangle_it 1.257 r_mcbond_it 0.701 r_nbtor_refined 0.32 r_nbd_refined 0.293 r_symmetry_vdw_refined 0.266 r_xyhbond_nbd_refined 0.231 r_symmetry_hbond_refined 0.204 r_chiral_restr 0.117 r_metal_ion_refined 0.106 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1328 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction CCP4 data scaling AMoRE phasing