☰ Navigation Tabs
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 VAPOR DIFFUSION 5.5 293 0.1 M Bis-Tris, 0.5% polyvinylpyrrolidone and 16% of PEG400, VAPOR DIFFUSION, temperature 293K, pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.3 46.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.88 α = 90 b = 115.311 β = 112.5 c = 130.243 γ = 90
Symmetry Space Group P 1 21 1
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 2007-10-01 SINGLE WAVELENGT
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8148 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 2.326 65.094 100 0.061 0.061 20.3 4.6 80299 80299 66.976
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 2.7 2.85 100 0.388 0.388 1.9 4.6 11696
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 MR THROUGHOUT 1knv 2.7 65.09 80279 80279 7973 99.98 0.23372 0.234 0.23 0.2272 0.267 0.2648 RANDOM 54.404
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] -0.54 -0.54 -0.13 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.442 r_dihedral_angle_4_deg 21.622 r_dihedral_angle_3_deg 15.206 r_angle_other_deg 3.82 r_mcangle_it 2.099 r_scangle_it 1.878 r_dihedral_angle_1_deg 1.542 r_angle_refined_deg 1.288 r_mcbond_it 1.183 r_scbond_it 1.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.442 r_dihedral_angle_4_deg 21.622 r_dihedral_angle_3_deg 15.206 r_angle_other_deg 3.82 r_mcangle_it 2.099 r_scangle_it 1.878 r_dihedral_angle_1_deg 1.542 r_angle_refined_deg 1.288 r_mcbond_it 1.183 r_scbond_it 1.122 r_symmetry_vdw_other 0.312 r_nbd_other 0.273 r_nbd_refined 0.244 r_symmetry_vdw_refined 0.23 r_nbtor_refined 0.203 r_xyhbond_nbd_refined 0.156 r_symmetry_hbond_refined 0.115 r_xyhbond_nbd_other 0.11 r_nbtor_other 0.107 r_chiral_restr 0.089 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.005 r_bond_other_d r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18735 Nucleic Acid Atoms 3562 Solvent Atoms 359 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PDB_EXTRACT data extraction MAR345dtb data collection MOLREP phasing