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Crystal structure of Type IIF restriction endonuclease Bse634I with cognate DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KNV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 293 100mM Na-acetate pH 4.25-5.5, 10mM CaCl2 or CaAc2, 4-8% (w/v) of PEG8000, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 52.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.937 α = 90 b = 87.387 β = 90 c = 125.127 γ = 90
Symmetry Space Group P 21 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 CCD MAR555 2007-09-25 SINGLE WAVELENGT
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 2.336 55.556 90.6 0.054 0.054 22.8 4.6 30943
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 2.34 2.46 64.5 0.332 0.332 2.3 4.4
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1KNV 2.35 55.556 34081 27769 3156 91.58 0.2457 0.2403 0.29343 0.2628 RANDOM 42.628
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] -2.09 3.28 -1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.423 r_dihedral_angle_4_deg 18.681 r_dihedral_angle_3_deg 16.157 r_dihedral_angle_1_deg 5.304 r_scangle_it 1.816 r_angle_refined_deg 1.186 r_scbond_it 1.134 r_mcangle_it 0.786 r_mcbond_it 0.413 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.423 r_dihedral_angle_4_deg 18.681 r_dihedral_angle_3_deg 16.157 r_dihedral_angle_1_deg 5.304 r_scangle_it 1.816 r_angle_refined_deg 1.186 r_scbond_it 1.134 r_mcangle_it 0.786 r_mcbond_it 0.413 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4687 Nucleic Acid Atoms 526 Solvent Atoms 106 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PDB_EXTRACT data extraction MOLREP phasing