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DNA recognition domain of the cytosine modification-dependent restriction endonuclease LpnPI
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OC8 PDB ENTRY 4OC8, chain A, residues 6-22, 31-85, 97-208
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 0.16 M (NH4)2SO4, 0.08 M Na-HEPES, 20% w/v PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.88 57.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.037 α = 90 b = 82.037 β = 90 c = 152.829 γ = 120
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 2014-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.0012 MAX II I911-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.1 41.4 100 0.101 21.5 12.9 33984 33984 22.34
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.21 100 0.524 0.524 1.4 12.8 4959
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 PDB ENTRY 4OC8, chain A, residues 6-22, 31-85, 97-208 2.1 41.019 1.24 33984 33923 6585 99.99 0.1691 0.1658 0.1652 0.1986 0.1965 RANDOM 26.6084
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 12.377 f_angle_d 1.092 f_chiral_restr 0.061 f_bond_d 0.01 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3490 Nucleic Acid Atoms Solvent Atoms 422 Heterogen Atoms 16
Software Software Software Name Purpose SCALA data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction MxCuBE data collection XDS data reduction