☰ Navigation Tabs
Crystal structure of Type IIP restriction endonuclease Kpn2I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 Crystallization buffer: 0.1M NaHepes pH7.5, 1.4M ammonium sulfate and glycerol 10%.
Complex of Kpn2I with DNA was used at concentration 2-7.5mg/ml
Crystal Properties Matthews coefficient Solvent content 2.93 57.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.794 α = 90 b = 134.794 β = 90 c = 134.794 γ = 90
Symmetry Space Group I 21 3
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 2015-06-25 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.98019,0.98029,0.97789 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) Rrim I (All) Rpim I (All) 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 2.88 95.31 100 0.116 0.116 0.134 0.021 28.3 39.8 9398 62.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.88 3.04 100 0.537 0.537 0.555 0.093 7.3 34.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 MAD FREE R-VALUE 2.88 20 8353 959 99.59 0.21498 0.20944 0.2007 0.26398 0.256 RANDOM 56.086
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 r_dihedral_angle_2_deg 38.43 r_dihedral_angle_4_deg 17.796 r_dihedral_angle_3_deg 16.262 r_dihedral_angle_1_deg 5.586 r_scangle_it 1.941 r_scbond_it 1.216 r_angle_refined_deg 1.14 r_mcangle_it 1.081 r_mcbond_it 0.579 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.43 r_dihedral_angle_4_deg 17.796 r_dihedral_angle_3_deg 16.262 r_dihedral_angle_1_deg 5.586 r_scangle_it 1.941 r_scbond_it 1.216 r_angle_refined_deg 1.14 r_mcangle_it 1.081 r_mcbond_it 0.579 r_nbtor_refined 0.315 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.15 r_xyhbond_nbd_refined 0.118 r_symmetry_hbond_refined 0.115 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_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 2452 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling Auto-Rickshaw phasing