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5hmC specific restriction endonuclease PvuRTs1I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 10% w/v PEG4000, 20% v/v glycerol, 20 mM D-glucose, 20 mM D-mannose, 20 mM D-galactose, 20 mM L-fucose, 20 mM D-xylose, 20 mM N-acetyl-D-glucosamine, 0.1 M MOPS/HEPES sodium, pH 7.5, for cryoprotection, crystals were transferred to a variant of the buffer with 28% v/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.83 56.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.99 α = 90 b = 61.99 β = 90 c = 210.99 γ = 90
Symmetry Space Group P 41 21 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 PIXEL DECTRIS PILATUS 6M 2013-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97630 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.35 50 96.6 0.048 0.048 19.5 5.7 17509 17509
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 2.35 2.41 99 0.97 0.97 2.2 5.9 1275
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.35 43.83 17495 17495 897 96.95 0.20563 0.20563 0.20305 0.25397 0.2653 RANDOM 70.387
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] 0.85 0.85 -1.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.515 r_dihedral_angle_4_deg 20.592 r_dihedral_angle_3_deg 17.299 r_dihedral_angle_1_deg 5.851 r_scangle_it 2.765 r_scbond_it 1.646 r_angle_refined_deg 1.293 r_mcangle_it 1.108 r_angle_other_deg 0.64 r_mcbond_it 0.577
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.515 r_dihedral_angle_4_deg 20.592 r_dihedral_angle_3_deg 17.299 r_dihedral_angle_1_deg 5.851 r_scangle_it 2.765 r_scbond_it 1.646 r_angle_refined_deg 1.293 r_mcangle_it 1.108 r_angle_other_deg 0.64 r_mcbond_it 0.577 r_mcbond_other 0.095 r_chiral_restr 0.069 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_gen_planes_other 0.001 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2469 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 15
Software Software Software Name Purpose SHELXDE phasing DM model building PHENIX model building REFMAC refinement XDS data reduction XSCALE data scaling DM phasing PHENIX phasing