☰ Navigation Tabs
2009 H1N1 PA endonuclease domain
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 2.3 46.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.619 α = 90 b = 73.619 β = 90 c = 129.056 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 2014-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97918 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 2.05 50 100 0.089 0.091 0.016 10 33 13811
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 2.05 2.12 100 0.714 0.727 0.133 0.977 29.4 1328
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 2.05 43 13079 689 99.94 0.1995 0.1977 0.2064 0.2332 0.2395 RANDOM 40.469
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] -0.63 -0.32 -0.63 2.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.353 r_dihedral_angle_4_deg 15.408 r_dihedral_angle_3_deg 12.435 r_dihedral_angle_1_deg 5.383 r_mcangle_it 2.324 r_mcbond_it 1.449 r_mcbond_other 1.444 r_angle_refined_deg 1.317 r_angle_other_deg 0.948 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.353 r_dihedral_angle_4_deg 15.408 r_dihedral_angle_3_deg 12.435 r_dihedral_angle_1_deg 5.383 r_mcangle_it 2.324 r_mcbond_it 1.449 r_mcbond_other 1.444 r_angle_refined_deg 1.317 r_angle_other_deg 0.948 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1445 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 2
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing