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2009 H1N1 PA endonuclease mutant F105S in complex with dTMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5D2O PDB entry 5D2O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 0.2 M magnesium chloride, 2 mM manganese chloride, 0.1 M Tris, pH 8.5, 30% w/v PEG4000
Crystal Properties Matthews coefficient Solvent content 2.36 47.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.084 α = 90 b = 74.084 β = 90 c = 130.312 γ = 120
Symmetry Space Group P 64 2 2
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 RAYONIX MX300-HS 2015-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (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 2 50 98.7 0.067 0.069 0.018 11.8 14 14714
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 92.1 0.893 0.931 0.255 0.759 11.6 1330
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 5D2O 2 50 13931 761 98.42 0.1852 0.1824 0.2004 0.2369 0.2366 RANDOM 47.191
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] -0.91 -0.46 -0.91 2.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.032 r_dihedral_angle_4_deg 16.787 r_dihedral_angle_3_deg 15.753 r_dihedral_angle_1_deg 6.539 r_mcangle_it 3.873 r_mcbond_it 2.801 r_mcbond_other 2.798 r_angle_refined_deg 2.218 r_angle_other_deg 1.163 r_chiral_restr 0.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.032 r_dihedral_angle_4_deg 16.787 r_dihedral_angle_3_deg 15.753 r_dihedral_angle_1_deg 6.539 r_mcangle_it 3.873 r_mcbond_it 2.801 r_mcbond_other 2.798 r_angle_refined_deg 2.218 r_angle_other_deg 1.163 r_chiral_restr 0.125 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1438 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 23
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing