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2009 H1N1 PA endonuclease mutant E119D in complex with L-742,001
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CZN PDB entry 5CZN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 0.1 M HEPES sodium, pH 7.5, 1.0 M ammonium sulfate, 2% w/v PEG400, 50 mM magnesium chloride, 50 mM manganese chloride
Crystal Properties Matthews coefficient Solvent content 2.93 57.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.881 α = 90 b = 89.881 β = 90 c = 134.148 γ = 90
Symmetry Space Group I 4 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 2014-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97921 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 2.29 50 99.6 0.062 0.064 0.018 10.8 12.4 12715
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 2.29 2.37 95.9 0.819 0.864 0.267 0.792 9.6 1219
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 5CZN 2.29 46 12091 622 99.55 0.2003 0.1982 0.2069 0.2408 0.241 RANDOM 65.79
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] 1.06 1.06 -2.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.759 r_dihedral_angle_3_deg 17.981 r_dihedral_angle_4_deg 16.89 r_dihedral_angle_1_deg 7.901 r_mcangle_it 4.83 r_mcbond_it 3.199 r_mcbond_other 3.183 r_angle_refined_deg 2.371 r_angle_other_deg 1.246 r_chiral_restr 0.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.759 r_dihedral_angle_3_deg 17.981 r_dihedral_angle_4_deg 16.89 r_dihedral_angle_1_deg 7.901 r_mcangle_it 4.83 r_mcbond_it 3.199 r_mcbond_other 3.183 r_angle_refined_deg 2.371 r_angle_other_deg 1.246 r_chiral_restr 0.133 r_bond_refined_d 0.026 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1403 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 24
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing