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Restriction endonuclease DPNI in complex with two DNA molecules
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ESJ PDB ENTRY 4ESJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 160 mM CALCIUM ACETATE, 80 mM SODIUM CACODYLATE PH 6.5, 14.4% W/V PEG 8000, 20% V/V GLYCEROL, 10 mM SPERMIDINE., VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.28 62.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.7 α = 90 b = 101.05 β = 90 c = 114.85 γ = 90
Symmetry Space Group C 2 2 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 PIXEL PSI PILATUS 6M 2012-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 1.23953 PETRA III, EMBL c/o DESY P14 (MX2)
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 99.7 0.049 0.049 20.51 6.37 23502 23502
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 99.9 0.44 0.44 4.14 6.68 1720
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4ESJ 2.35 46.23 23477 23477 1204 99.72 0.20216 0.20216 0.20125 0.1964 0.21904 0.212 RANDOM 43.385
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] -0.77 -0.42 1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.887 r_dihedral_angle_4_deg 19.589 r_dihedral_angle_3_deg 15.495 r_dihedral_angle_1_deg 6.217 r_angle_other_deg 3.804 r_scangle_it 2.848 r_scbond_it 1.794 r_angle_refined_deg 1.34 r_mcangle_it 1.282 r_mcbond_it 0.675
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.887 r_dihedral_angle_4_deg 19.589 r_dihedral_angle_3_deg 15.495 r_dihedral_angle_1_deg 6.217 r_angle_other_deg 3.804 r_scangle_it 2.848 r_scbond_it 1.794 r_angle_refined_deg 1.34 r_mcangle_it 1.282 r_mcbond_it 0.675 r_nbd_other 0.273 r_symmetry_vdw_other 0.222 r_metal_ion_refined 0.218 r_symmetry_hbond_refined 0.212 r_nbtor_refined 0.201 r_nbd_refined 0.197 r_xyhbond_nbd_refined 0.189 r_symmetry_vdw_refined 0.14 r_nbtor_other 0.109 r_chiral_restr 0.083 r_xyhbond_nbd_other 0.071 r_gen_planes_refined 0.012 r_bond_refined_d 0.011 r_gen_planes_other 0.01 r_bond_other_d r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2096 Nucleic Acid Atoms 812 Solvent Atoms 94 Heterogen Atoms 3
Software Software Software Name Purpose MOLREP phasing ARP/wARP model building REFMAC refinement XDS data reduction XSCALE data scaling