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N-terminal domain of a human Coronavirus NL63 nucleocapsid protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BXX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 AMMONIUM SULPHATE, TRIS, PH 8.5, VAPOR
DIFFUSION, SITTING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 1.95 36.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.09 α = 90 b = 48.09 β = 90 c = 101.22 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 2014-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.92 BESSY 14.1
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 1.49 50.61 99.1 0.034 16.1 2.9 42346
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 1.49 1.53 99.5 0.095 7.4 2.9
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 2BXX 1.49 41.65 40174 2132 99.1 0.153 0.151 0.1522 0.197 0.1973 RANDOM 21.82
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] 0.02 0.01 0.02 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.17 r_dihedral_angle_4_deg 23.638 r_dihedral_angle_3_deg 15.684 r_dihedral_angle_1_deg 8.949 r_long_range_B_refined 7.575 r_long_range_B_other 7.303 r_scangle_other 4.674 r_mcangle_it 3.852 r_mcangle_other 3.852 r_scbond_it 3.232
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.17 r_dihedral_angle_4_deg 23.638 r_dihedral_angle_3_deg 15.684 r_dihedral_angle_1_deg 8.949 r_long_range_B_refined 7.575 r_long_range_B_other 7.303 r_scangle_other 4.674 r_mcangle_it 3.852 r_mcangle_other 3.852 r_scbond_it 3.232 r_scbond_other 3.145 r_angle_refined_deg 2.533 r_mcbond_it 2.425 r_mcbond_other 2.421 r_angle_other_deg 1.083 r_chiral_restr 0.152 r_bond_refined_d 0.024 r_gen_planes_refined 0.012 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 2063 Nucleic Acid Atoms Solvent Atoms 356 Heterogen Atoms 70
Software Software Software Name Purpose iMOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement