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Crystal structure of Ebola glycoprotein in complex with ibuprofen
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JQ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 9% (w/v) PEG 6000 and 0.1 M Sodium citrate tribasic dihydrate
Crystal Properties Matthews coefficient Solvent content 3.49 64.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.76 α = 90 b = 113.76 β = 90 c = 306.15 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2015-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9700 Diamond I02
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 2.68 82.84 99.9 0.129 14.7 9.8 21842
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.68 2.75 100 1.5 8.3
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 5JQ3 2.68 82.84 20734 1107 99.9 0.201 0.199 0.2004 0.234 0.2346 RANDOM 73.22
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 0.37 0.73 -2.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.628 r_dihedral_angle_4_deg 16.894 r_dihedral_angle_3_deg 13.758 r_dihedral_angle_1_deg 6.468 r_long_range_B_refined 5.972 r_long_range_B_other 5.971 r_scangle_other 3.014 r_mcangle_it 2.779 r_mcangle_other 2.778 r_scbond_it 1.709
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.628 r_dihedral_angle_4_deg 16.894 r_dihedral_angle_3_deg 13.758 r_dihedral_angle_1_deg 6.468 r_long_range_B_refined 5.972 r_long_range_B_other 5.971 r_scangle_other 3.014 r_mcangle_it 2.779 r_mcangle_other 2.778 r_scbond_it 1.709 r_scbond_other 1.709 r_mcbond_it 1.522 r_mcbond_other 1.522 r_angle_refined_deg 1.241 r_angle_other_deg 0.871 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 3025 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing