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2009 H1N1 PA endonuclease in complex with dTMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4E5E PDB entry 4E5E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 0.2 M magnesium chloride, 5 mM manganese chloride, 0.1 M Tris, pH 8.5, 30% w/v PEG4000
Crystal Properties Matthews coefficient Solvent content 2.31 46.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.908 α = 90 b = 73.908 β = 90 c = 128.282 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 MARMOSAIC 225 mm CCD 2014-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0000 APS 22-BM
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 2.1 64.006 100 0.119 0.121 0.022 6 28.4 12747
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 2.1 2.18 100 0.965 0.982 0.179 0.92 28.1 1243
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 4E5E 2.1 50.01 12084 623 99.85 0.1747 0.1712 0.1824 0.2438 0.2449 RANDOM 37.181
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] -0.47 -0.23 -0.47 1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.495 r_dihedral_angle_4_deg 21.032 r_dihedral_angle_3_deg 15.914 r_dihedral_angle_1_deg 6.372 r_mcangle_it 3.295 r_mcbond_it 2.221 r_mcbond_other 2.216 r_angle_refined_deg 2.198 r_angle_other_deg 1.194 r_chiral_restr 0.162
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.495 r_dihedral_angle_4_deg 21.032 r_dihedral_angle_3_deg 15.914 r_dihedral_angle_1_deg 6.372 r_mcangle_it 3.295 r_mcbond_it 2.221 r_mcbond_other 2.216 r_angle_refined_deg 2.198 r_angle_other_deg 1.194 r_chiral_restr 0.162 r_bond_refined_d 0.025 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1458 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing