☰ Navigation Tabs
bifunctional endonuclease in complex with ssDNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CWM PDB ENTRY 4CWM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.1 M HEPES PH 7.5, 0.2 M LI2SO4, 30% (W/V) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.87 57.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.902 α = 90 b = 66.159 β = 90 c = 98.148 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 100 CCD ADSC QUANTUM 315 MIRRORS 2012-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.67 50 94.8 0.06 28.9 9.9 39430 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 1.74 95.7 0.71 2.2 9.5
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4CWM 1.67 27.98 36995 1970 94.6 0.14261 0.14002 0.152 0.19145 0.1952 RANDOM 27.7
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] -1.23 0.02 1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.916 r_sphericity_free 30.797 r_dihedral_angle_3_deg 13.404 r_dihedral_angle_4_deg 13.294 r_sphericity_bonded 10.649 r_dihedral_angle_1_deg 5.508 r_scbond_it 3.375 r_mcangle_it 2.909 r_mcbond_it 2.494 r_mcbond_other 2.493
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.916 r_sphericity_free 30.797 r_dihedral_angle_3_deg 13.404 r_dihedral_angle_4_deg 13.294 r_sphericity_bonded 10.649 r_dihedral_angle_1_deg 5.508 r_scbond_it 3.375 r_mcangle_it 2.909 r_mcbond_it 2.494 r_mcbond_other 2.493 r_rigid_bond_restr 2.35 r_angle_refined_deg 1.47 r_angle_other_deg 0.821 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other 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 2014 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 221
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing