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Crystal structure from SARS-CoV-2 NendoU NSP15
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6X1B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293 20 % w/v Polyethylene glycol 3350, 100 mM BIS-TRIS propane, pH 6.5, 200 mM Sodium sulfate
Crystal Properties Matthews coefficient Solvent content 4.68 73.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.92 α = 90 b = 150.92 β = 90 c = 111.1 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 EIGER X 16M 2020-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.9794 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.59 84.65 94.8 1.031 1.049 0.192 0.99 7.6 29.8 37814 63.68
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.59 2.743 60.3 3.288 3.345 0.608 0.373 30.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6x1b 2.59 84.65 37814 1858 84.3 0.189 0.187 0.22 0.2252 RANDOM 57.8
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] -5.3501 -5.3501 10.7003
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.83 t_omega_torsion 3.08 t_angle_deg 1.2 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.83 t_omega_torsion 3.08 t_angle_deg 1.2 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5496 Nucleic Acid Atoms Solvent Atoms 468 Heterogen Atoms 48
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction PHASER phasing