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Structure of the NSP3 X-domain of human coronavirus NL63
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ACF PDB ENTRY 2ACF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.2 44.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.97 α = 90 b = 54.77 β = 90 c = 57.33 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH MIRRORS 2006-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
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 1.7 40 99 0.1 8.7 5.5 19914 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 1.7 1.74 88.3 0.95 1.64 4.2
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 PDB ENTRY 2ACF 1.9 39.59 12892 990 99.8 0.189 0.185 0.1849 0.243 0.2424 RANDOM 21.25
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] 0.93 1.34 -2.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.082 r_dihedral_angle_3_deg 13.902 r_dihedral_angle_4_deg 13.357 r_dihedral_angle_1_deg 7.453 r_scangle_it 3.906 r_scbond_it 2.532 r_mcangle_it 1.604 r_angle_refined_deg 1.52 r_mcbond_it 0.935 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.082 r_dihedral_angle_3_deg 13.902 r_dihedral_angle_4_deg 13.357 r_dihedral_angle_1_deg 7.453 r_scangle_it 3.906 r_scbond_it 2.532 r_mcangle_it 1.604 r_angle_refined_deg 1.52 r_mcbond_it 0.935 r_nbtor_refined 0.315 r_symmetry_vdw_refined 0.262 r_nbd_refined 0.22 r_symmetry_hbond_refined 0.159 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.103 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1320 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement HKL data reduction SCALEPACK data scaling PHASER phasing