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2009 H1N1 PA endonuclease mutant F105S in complex with rUMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5D42
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 2.33 47.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.783 α = 90 b = 73.783 β = 90 c = 129.879 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 2.08 50 99.6 0.082 0.085 0.022 11.7 13.9 13123
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 2.08 2.18 99.1 0.83 0.867 0.239 0.662 12.6 1274
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 5D42 2.08 50 12412 690 99.52 0.1832 0.1805 0.1971 0.2315 0.2312 RANDOM 48.278
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] -0.73 -0.37 -0.73 2.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.545 r_dihedral_angle_4_deg 19.11 r_dihedral_angle_3_deg 15.461 r_dihedral_angle_1_deg 6.42 r_mcangle_it 3.768 r_mcbond_it 2.724 r_mcbond_other 2.723 r_angle_refined_deg 2.222 r_angle_other_deg 1.135 r_chiral_restr 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.545 r_dihedral_angle_4_deg 19.11 r_dihedral_angle_3_deg 15.461 r_dihedral_angle_1_deg 6.42 r_mcangle_it 3.768 r_mcbond_it 2.724 r_mcbond_other 2.723 r_angle_refined_deg 2.222 r_angle_other_deg 1.135 r_chiral_restr 0.127 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1448 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 23
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing