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Crystal Structure of Marburg virus VP40 Dimer
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 17.5% ethanol, 75mM NaCl, 10mM CHAPS, 100mM Tris-HCl, pH 7.7
Crystal Properties Matthews coefficient Solvent content 2.28 45.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.81 α = 90 b = 107.31 β = 90 c = 127.65 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 100 CCD MARMOSAIC 300 mm CCD 2012-08-19 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.979, 0.980 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.81 50 99.5 6.9 4 25037
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.81 29.67 15475 828 99 0.20459 0.20182 0.2141 0.25686 0.2697 RANDOM 42.378
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] -0.04 -0.01 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.721 r_dihedral_angle_4_deg 23.713 r_dihedral_angle_3_deg 14.759 r_dihedral_angle_1_deg 6.579 r_long_range_B_refined 5.721 r_long_range_B_other 5.721 r_mcangle_it 2.431 r_mcangle_other 2.431 r_scangle_other 2.176 r_angle_refined_deg 1.546
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.721 r_dihedral_angle_4_deg 23.713 r_dihedral_angle_3_deg 14.759 r_dihedral_angle_1_deg 6.579 r_long_range_B_refined 5.721 r_long_range_B_other 5.721 r_mcangle_it 2.431 r_mcangle_other 2.431 r_scangle_other 2.176 r_angle_refined_deg 1.546 r_mcbond_it 1.391 r_mcbond_other 1.388 r_scbond_it 1.281 r_scbond_other 1.281 r_angle_other_deg 1.09 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.004 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4033 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling Auto-Rickshaw phasing