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Structural distortions in psoralen cross-linked DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FHY pdb entry 1FHY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 0.5 mM HMT-d(CCGCTAGCGG), 30 mM NaCacodylate (pH = 7.0), 25 mM calcium chloride and 5% 2-methyl-2,4-pentanediol (MPD) against a 30 mL reservoir solution of 15% MPD (boosted to 20% two weeks later), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.12 41.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.007 α = 90 b = 22.496 β = 128.8 c = 44.67 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD ADSC QUANTUM 4 2003-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
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 1.5 26.89 83 0.081 18.2 7306 7306
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) 1.5 1.59 50.2 0.628 1.4 653
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1FHY 1.5 26.89 7306 6518 788 100 0.21549 0.20995 0.2103 0.26162 0.2608 RANDOM 16.589
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] -0.79 -0.4 0.8 -0.5
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 3.111 r_scangle_it 3.041 r_scbond_it 2.5 r_nbd_refined 0.366 r_nbtor_refined 0.326 r_metal_ion_refined 0.314 r_xyhbond_nbd_refined 0.29 r_symmetry_vdw_refined 0.275 r_symmetry_hbond_refined 0.219 r_symmetry_metal_ion_refined 0.188
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 3.111 r_scangle_it 3.041 r_scbond_it 2.5 r_nbd_refined 0.366 r_nbtor_refined 0.326 r_metal_ion_refined 0.314 r_xyhbond_nbd_refined 0.29 r_symmetry_vdw_refined 0.275 r_symmetry_hbond_refined 0.219 r_symmetry_metal_ion_refined 0.188 r_chiral_restr 0.137 r_mcbond_it 0.054 r_bond_refined_d 0.016 r_gen_planes_refined 0.016 r_bond_other_d r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_mcbond_other r_mcangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 404 Solvent Atoms 194 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling EPMR phasing