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Neutron crystal structure of SARS-CoV-2 NSP3 macrodomain at 293 K (P43 crystal form)
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KQO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 293 100 mM CHES pH 9.5, 34% PEG 3000
Crystal Properties Matthews coefficient Solvent content 2.21 44.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.328 α = 90 b = 89.328 β = 90 c = 40.349 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL DECTRIS EIGER R 4M OSMIC VARIMAX 2021-03-29 M SINGLE WAVELENGTH 2 1 neutron 293 AREA DETECTOR ORNL ANGER CAMERA COLLIMATORS 2021-03-15 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54 2 SPALLATION SOURCE ORNL Spallation Neutron Source BEAMLINE MANDI 2.00-4.00 ORNL Spallation Neutron Source MANDI
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 1.6 28.39 99.6 0.087 0.038 0.996 15.6 5.9 42240 2 1.89 14.12 94 0.217 0.101 0.926 7.2 4.4 24142
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 0.265 0.874 4.6 2.8 2 1.89 1.96 0.2524 0.411 2.7 3.1
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.6 23.14 42212 2042 99.63 0.1239 0.124 0.1576 0.1575 RANDOM 22.64 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 1.89 14.12 24141 1173 94.01 0.2258 0.275 RANDOM 22.64
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.8052 f_dihedral_angle_d 20.8052 f_angle_d 1.474 f_angle_d 1.474 f_chiral_restr 0.0809 f_chiral_restr 0.0809 f_bond_d 0.0119 f_bond_d 0.0119 f_plane_restr 0.0092 f_plane_restr 0.0092
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2535 Nucleic Acid Atoms Solvent Atoms 322 Heterogen Atoms 13
Software Software Software Name Purpose PHENIX refinement Mantid data reduction LAUENORM data scaling PHASER phasing Coot model building