☰ Navigation Tabs
Crystal structure of ERI2 nuclease bound to rAMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4L83
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 288 9% MPEG 2K,
1% saturated Magnesium Sulfate,
5% Ethylene glycol,
200 mM Imidazole Malate buffer pH 5.4
Crystal Properties Matthews coefficient Solvent content 2.1 41.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.832 α = 90 b = 56.338 β = 104.572 c = 75.852 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2017-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 12.3.1 1.11583 ALS 12.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.35 50 90.8 0.104 27.9 4.7 19057 48.79
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.39 0.55
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4l83 2.35 44.69 31205 1529 76.97 0.1812 0.179 0.1796 0.2227 0.2229 75.72
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.0929 f_angle_d 0.5394 f_chiral_restr 0.0408 f_plane_restr 0.0036 f_bond_d 0.0022
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3429 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing