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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 1G1J PDB CODE 1G1J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 1.5M lithium sulphate monohydrate, 0.1 HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.1 41.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.692 α = 90 b = 38.09 β = 90 c = 182.354 γ = 90
Symmetry Space Group I 2 2 2
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 system 2004-11-06 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 1.67 15 98.8 0.045 29.8 7.1 12801
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 1.67 1.76 95.5 0.142 12.5 1776
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 PDB CODE 1G1J 1.67 15 12178 623 98.82 0.18973 0.18764 0.2003 0.23318 0.2448 RANDOM 21.486
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] -0.03 0.22 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.028 r_dihedral_angle_3_deg 14.499 r_dihedral_angle_4_deg 11.405 r_scangle_it 3.459 r_dihedral_angle_1_deg 3.403 r_scbond_it 2.278 r_mcangle_it 1.446 r_angle_refined_deg 1.117 r_mcbond_it 0.987 r_angle_other_deg 0.765
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.028 r_dihedral_angle_3_deg 14.499 r_dihedral_angle_4_deg 11.405 r_scangle_it 3.459 r_dihedral_angle_1_deg 3.403 r_scbond_it 2.278 r_mcangle_it 1.446 r_angle_refined_deg 1.117 r_mcbond_it 0.987 r_angle_other_deg 0.765 r_mcbond_other 0.239 r_symmetry_vdw_other 0.232 r_symmetry_hbond_refined 0.208 r_nbd_refined 0.199 r_nbtor_refined 0.168 r_symmetry_vdw_refined 0.159 r_nbd_other 0.148 r_xyhbond_nbd_refined 0.137 r_nbtor_other 0.081 r_chiral_restr 0.064 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 700 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction CCP4 data scaling AMoRE phasing