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Crystal structure of Marburg virus VP35 RNA binding domain bound to 12-bp dsRNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GH9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.1 M Bis-Tris, 2% v/v Tacsimate, 18% PEG 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.04 39.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.593 α = 90 b = 99.191 β = 89.92 c = 81.801 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD ADSC QUANTUM 315r Double-crystal, Si(111) liquid N2 cooled 2011-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0000 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.5 81.8 0.131 0.131 8.5 2.5 20261 1 1 17
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.501 2.566 100 0.362 0.362 2.2 2.5 988
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 4GH9 2.5 81.8 1 1 18981 1017 98.7 0.21073 0.21073 0.20867 0.2127 0.24987 0.2525 RANDOM 17
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] 0.12 0.36 -1.3 1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.227 r_dihedral_angle_3_deg 9.955 r_dihedral_angle_4_deg 9.247 r_dihedral_angle_1_deg 2.748 r_scangle_it 1.541 r_mcangle_it 1.153 r_scbond_it 0.845 r_mcbond_it 0.632 r_rigid_bond_restr 0.561 r_angle_refined_deg 0.448
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.227 r_dihedral_angle_3_deg 9.955 r_dihedral_angle_4_deg 9.247 r_dihedral_angle_1_deg 2.748 r_scangle_it 1.541 r_mcangle_it 1.153 r_scbond_it 0.845 r_mcbond_it 0.632 r_rigid_bond_restr 0.561 r_angle_refined_deg 0.448 r_chiral_restr 0.028 r_bond_refined_d 0.001 r_gen_planes_refined 0.001 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3772 Nucleic Acid Atoms 504 Solvent Atoms 156 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling