☰ Navigation Tabs
Crystal structure of the I-SmaMI LAGLIDADG homing endonuclease bound to cleaved DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QQY PDB ENTRY 3QQY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 20% PEG550 MME, 50mM magnesium chloride, 0.1M TrisHCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.05 40.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.284 α = 90 b = 67.429 β = 90 c = 98.09 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 170 IMAGE PLATE RIGAKU RAXIS IV++ 2012-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.98 30 91.5 0.054 13.52 2.9 26452 29068 1 2.92
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.06 55.3 0.3 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MIR THROUGHOUT PDB ENTRY 3QQY 1.98 29.56 25028 1334 91.08 0.19059 0.18606 0.1861 0.27697 0.2734 RANDOM 37.069
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] 2.56 -0.57 -2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.231 r_sphericity_free 24.822 r_dihedral_angle_3_deg 18.959 r_dihedral_angle_4_deg 13.06 r_sphericity_bonded 10.729 r_dihedral_angle_1_deg 6.489 r_rigid_bond_restr 3.343 r_angle_refined_deg 1.691 r_chiral_restr 0.122 r_bond_refined_d 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.231 r_sphericity_free 24.822 r_dihedral_angle_3_deg 18.959 r_dihedral_angle_4_deg 13.06 r_sphericity_bonded 10.729 r_dihedral_angle_1_deg 6.489 r_rigid_bond_restr 3.343 r_angle_refined_deg 1.691 r_chiral_restr 0.122 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2391 Nucleic Acid Atoms 1021 Solvent Atoms 116 Heterogen Atoms 2
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling