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High resolution crystal structure of domain III of E1 fusion glycoprotein of Semliki Forest Virus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RER PDB ENTRY 1RER (DOMAIN III)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 25% PEG 8K, 0.2M NA ACETATE, 0.1M CACO PH 6.5, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2 37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.343 α = 90 b = 62.659 β = 90 c = 113.735 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 120 CCD ADSC CCD 2005-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 28.57 98.8 0.05 23.7 4.4 31583
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 1.5 1.55 95.9 0.56 3.9
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 ENTRY 1RER (DOMAIN III) 1.55 28.57 29589 1579 98.7 0.199 0.198 0.2005 0.226 0.2274 RANDOM 26.05
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 27.912 r_dihedral_angle_2_deg 24.759 r_dihedral_angle_3_deg 11.205 r_dihedral_angle_1_deg 7.412 r_scbond_it 4.694 r_scangle_it 4.115 r_mcangle_it 2.026 r_angle_refined_deg 1.369 r_mcbond_it 1.193 r_symmetry_vdw_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 27.912 r_dihedral_angle_2_deg 24.759 r_dihedral_angle_3_deg 11.205 r_dihedral_angle_1_deg 7.412 r_scbond_it 4.694 r_scangle_it 4.115 r_mcangle_it 2.026 r_angle_refined_deg 1.369 r_mcbond_it 1.193 r_symmetry_vdw_refined 0.313 r_nbtor_refined 0.284 r_nbd_refined 0.199 r_symmetry_hbond_refined 0.157 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.084 r_bond_refined_d 0.01 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_refined 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1300 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing