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Crystal structure of pre-specific restriction endonuclease AgeI-DNA complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 0.2 M NaCl, 0.1 M Bis-Tris (pH 5.5), 19% PEG3350 2 VAPOR DIFFUSION, SITTING DROP 5.5 291 0.2 M NaCl, 0.1 M Bis-Tris (pH 5.5), 19% PEG3350
Crystal Properties Matthews coefficient Solvent content 1.97 37.65 1.97 37.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.003 α = 90 b = 79.806 β = 90 c = 101.655 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 2008-12-08 M SINGLE WAVELENGTH 2 2 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2009-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.99985 EMBL/DESY, HAMBURG X12 2 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.5 79.809 97.8 0.062 0.062 0.066 0.017 24.7 8.2 84560 84560 15.32
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 1.5 1.58 100 0.197 0.197 0.107 3.8 5 12458
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD FREE R-VALUE 1.5 40.27 1.28 84472 8036 96.19 0.155 0.1517 0.1551 0.1852 0.189 Random selection 22.6389
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 16.726 f_angle_d 1.022 f_chiral_restr 0.04 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4271 Nucleic Acid Atoms 444 Solvent Atoms 524 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MLPHARE phasing MOLREP phasing DM phasing Coot model building PHENIX refinement PDB_EXTRACT data extraction