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Crystal structure of restriction endonuclease AgeI
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DWB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 Crystallization buffer was 0.1 M NaCl, 0.1
M Na-Hepes (pH 7.5), 22% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.18 43.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.213 α = 90 b = 59.269 β = 90 c = 120.915 γ = 90
Symmetry Space Group P 21 21 21
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 mirrors 2014-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 0.9100 MAX II I911-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.5 33.329 100 0.118 0.141 0.057 12.5 5.8 9795 9795 31.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 100 0.647 0.647 0.312 1.1 5.9 1376
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 5DWB 2.5 33.329 1.38 9756 867 99.99 0.2186 0.2142 0.2217 0.256 0.2592 Random selection 36.9635
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 13.22 f_angle_d 0.676 f_chiral_restr 0.026 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2126 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms
Software Software Software Name Purpose MxCuBE data collection MOSFLM data reduction SCALA data scaling MOLREP phasing Coot model building PHENIX refinement PDB_EXTRACT data extraction