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2009 H1N1 PA endonuclease in complex with L-742,001
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4E5E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 0.2 M MgCl2, 5mM MnCl2, 0.1 M Tris pH 8.5, 30%(w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.39 48.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.899 α = 90 b = 73.899 β = 90 c = 127.457 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 2014-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 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 2.17 50 99.8 0.128 0.133 0.037 6.6 12.8 11511
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 2.17 2.25 98.3 0.893 0.952 0.319 0.763 8.1 1090
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 4E5E 2.17 50 10926 549 99.78 0.20242 0.19872 0.2079 0.28166 0.2819 RANDOM 38.33
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] -0.87 -0.44 -0.87 2.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.652 r_dihedral_angle_3_deg 19.052 r_dihedral_angle_4_deg 18.307 r_dihedral_angle_1_deg 7.658 r_long_range_B_refined 6.668 r_long_range_B_other 6.627 r_scangle_other 4.494 r_mcangle_it 3.442 r_mcangle_other 3.442 r_scbond_it 2.772
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.652 r_dihedral_angle_3_deg 19.052 r_dihedral_angle_4_deg 18.307 r_dihedral_angle_1_deg 7.658 r_long_range_B_refined 6.668 r_long_range_B_other 6.627 r_scangle_other 4.494 r_mcangle_it 3.442 r_mcangle_other 3.442 r_scbond_it 2.772 r_scbond_other 2.765 r_mcbond_it 2.151 r_mcbond_other 2.145 r_angle_refined_deg 2.108 r_angle_other_deg 1.207 r_chiral_restr 0.132 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1452 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing