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Crystal structure of the macro domain in Middle-East Respiratory Syndrome Coronavirus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FAV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 1.3 M sodium citrate tribasic dihydrate,
0.1 M Bis-Tris propane pH7.0.
Crystal Properties Matthews coefficient Solvent content 2.64 53.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.58 α = 90 b = 65.17 β = 90 c = 90.76 γ = 90
Symmetry Space Group P 2 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2013-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033 PETRA III, DESY P11
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 1.66 52.94 99.7 0.061 23.9 12.3 22856 21709 15.5
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 1.66 1.75 99 0.177 8.9 12.1
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 2FAV 1.66 52.94 21709 1111 99.51 0.14272 0.14097 0.155 0.17669 0.1853 RANDOM 17.676
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] 0.45 -1.3 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.178 r_dihedral_angle_4_deg 23.382 r_dihedral_angle_3_deg 12.843 r_long_range_B_refined 8.548 r_long_range_B_other 8.216 r_dihedral_angle_1_deg 5.951 r_scangle_other 4.922 r_scbond_it 3.367 r_scbond_other 3.364 r_mcangle_it 2.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.178 r_dihedral_angle_4_deg 23.382 r_dihedral_angle_3_deg 12.843 r_long_range_B_refined 8.548 r_long_range_B_other 8.216 r_dihedral_angle_1_deg 5.951 r_scangle_other 4.922 r_scbond_it 3.367 r_scbond_other 3.364 r_mcangle_it 2.46 r_mcangle_other 2.46 r_angle_refined_deg 2.292 r_mcbond_it 1.725 r_mcbond_other 1.677 r_angle_other_deg 1.15 r_chiral_restr 0.128 r_bond_refined_d 0.023 r_gen_planes_refined 0.014 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 1242 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing