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Core Structure of S2 from the Human Coronavirus NL63 Spike Glycoprotein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZV8 PDB ENTRY 1ZV8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 298 PEG 400, sodium acetate, Imidazole, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.9 35.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.02 α = 90 b = 51.688 β = 107.56 c = 54.08 γ = 90
Symmetry Space Group P 1 21 1
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 2006-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4C 0.9795 NSLS X4C
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 1.747 51.57 95.6 0.068 10.7 3.2 25668 25668 20.2
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 1.747 1.81 98.1 0.363 3.7 3.1 2573
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT PDB ENTRY 1ZV8 1.747 51.57 25668 25668 1292 95.6 0.1986 0.19866 0.19643 0.1964 0.23977 0.241 RANDOM 23.486
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] 0.43 0.97 0.03 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.82 r_dihedral_angle_3_deg 14.962 r_scangle_it 5.963 r_dihedral_angle_1_deg 4.538 r_scbond_it 3.48 r_mcangle_it 2.051 r_angle_refined_deg 1.502 r_mcbond_it 1.145 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.223
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.82 r_dihedral_angle_3_deg 14.962 r_scangle_it 5.963 r_dihedral_angle_1_deg 4.538 r_scbond_it 3.48 r_mcangle_it 2.051 r_angle_refined_deg 1.502 r_mcbond_it 1.145 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.218 r_symmetry_hbond_refined 0.174 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.121 r_bond_refined_d 0.02 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2009 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 7
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MAR345 data collection DENZO data reduction SCALEPACK data scaling