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Crystal structure of Y2 I-AniI variant (F13Y/S111Y)/DNA complex with calcium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P8K PDB Entry 1P8K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 303 32% Polypropylene glycol P400, 0.08M Bis-Tris, 0.25M sodium chloride, 0.05M calucium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal Properties Matthews coefficient Solvent content 2.87 57.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.555 α = 90 b = 192.603 β = 90 c = 161.8 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD 2008-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.000 ALS 5.0.1
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 2.7 37.14 95.7 0.068 28.8 9.9 46294 44303
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 2.7 2.8 93.4 0.473 3.25 5.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB Entry 1P8K 2.7 37.14 43936 39630 2126 90.2 0.20057 0.1978 0.25316 0.2878 RANDOM 61.305
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] 0.21 -0.18 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.767 r_dihedral_angle_3_deg 20.277 r_dihedral_angle_4_deg 17.063 r_dihedral_angle_1_deg 6.062 r_angle_refined_deg 1.591 r_scangle_it 1.58 r_scbond_it 0.967 r_mcangle_it 0.89 r_mcbond_it 0.502 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.767 r_dihedral_angle_3_deg 20.277 r_dihedral_angle_4_deg 17.063 r_dihedral_angle_1_deg 6.062 r_angle_refined_deg 1.591 r_scangle_it 1.58 r_scbond_it 0.967 r_mcangle_it 0.89 r_mcbond_it 0.502 r_nbtor_refined 0.312 r_nbd_refined 0.237 r_symmetry_hbond_refined 0.22 r_symmetry_vdw_refined 0.204 r_xyhbond_nbd_refined 0.189 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6273 Nucleic Acid Atoms 3795 Solvent Atoms 67 Heterogen Atoms 6
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling