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Structure of an N-Terminal Truncated Form of Nendou (NSP15) From SARS-CORONAVIRUS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H85
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 0.2 M sodium bromide, 0.1 M sodium acetate, PH 5.5 and 25% PEG 2000MME, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.94 68.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.974 α = 90 b = 98.974 β = 90 c = 214.926 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 200 CCD MARMOSAIC 325 mm CCD MIRRORS 2006-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.9793 APS 23-ID-B
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 2.9 85.75 98.1 0.085 0.091 14.4 2.9 52135 52135
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) 2.9 2.97 89.9 0.466 0.491 1.44 1.9
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 2H85 2.9 85.75 48362 2601 97.85 0.24624 0.24337 0.2366 0.30068 0.2927 RANDOM 70.606
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] 4.53 2.27 4.53 -6.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.017 r_dihedral_angle_3_deg 21.757 r_dihedral_angle_4_deg 18.83 r_dihedral_angle_1_deg 7.453 r_scangle_it 1.926 r_angle_refined_deg 1.485 r_scbond_it 1.125 r_mcangle_it 1.069 r_mcbond_it 0.585 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.017 r_dihedral_angle_3_deg 21.757 r_dihedral_angle_4_deg 18.83 r_dihedral_angle_1_deg 7.453 r_scangle_it 1.926 r_angle_refined_deg 1.485 r_scbond_it 1.125 r_mcangle_it 1.069 r_mcbond_it 0.585 r_nbtor_refined 0.317 r_nbd_refined 0.242 r_symmetry_vdw_refined 0.188 r_xyhbond_nbd_refined 0.163 r_symmetry_hbond_refined 0.121 r_chiral_restr 0.1 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9402 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling PHASER phasing