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Crystal structure of Nsp15-H234A mutant- Hexamer in asymmetric unit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H85
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.9 289 at 10-15 mg/ml of protein in 0.05-0.1 M MgCl2, 3-5 % MPD and 0.1 M tri-sodium citrate dehydrate (pH 5.6-5.9). , VAPOR DIFFUSION, HANGING DROP, temperature 289K, pH 5.90
Crystal Properties Matthews coefficient Solvent content 3.37 63.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 305.757 α = 90 b = 305.757 β = 90 c = 88.74 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 CCD MAR CCD 165 mm 2004-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B APS 14-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.8 152.5 91.9 66521
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.8 2.87 78.2
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 (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 2H85 2.8 50 66521 66521 3507 91.96 0.20043 0.19788 0.206 0.25953 0.2566 RANDOM 60.345
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] 0.58 0.29 0.58 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.533 r_dihedral_angle_4_deg 19.552 r_dihedral_angle_3_deg 18.466 r_dihedral_angle_1_deg 5.816 r_scangle_it 2.122 r_scbond_it 1.334 r_mcangle_it 1.257 r_angle_refined_deg 1.067 r_mcbond_it 0.677 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.533 r_dihedral_angle_4_deg 19.552 r_dihedral_angle_3_deg 18.466 r_dihedral_angle_1_deg 5.816 r_scangle_it 2.122 r_scbond_it 1.334 r_mcangle_it 1.257 r_angle_refined_deg 1.067 r_mcbond_it 0.677 r_nbtor_refined 0.301 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.155 r_xyhbond_nbd_refined 0.126 r_symmetry_hbond_refined 0.107 r_chiral_restr 0.075 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16071 Nucleic Acid Atoms Solvent Atoms 441 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing