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Crystal structure of Fis bound to 27 bp DNA F25 containing T2A3 sequence at center
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IV5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 0.2 M Sodium citrate, 0.1 M TRIS-HCl pH 8.5, 38% PEG 400, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4 69.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.296 α = 90 b = 93.076 β = 90 c = 155.097 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 2008-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 1.000 APS 24-ID-C
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 3.1 90 91 0.186 7.4 3.9 10882
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 3.1 3.21 93.8 0.666 4 1068
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 3IV5 3.1 79.81 10795 512 90.03 0.245 0.242 0.2422 0.291 0.2857 RANDOM 82.247
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 45.751 r_dihedral_angle_4_deg 27.378 r_dihedral_angle_3_deg 17.914 r_dihedral_angle_1_deg 5.825 MAIN-CHAIN ANGLE REFINED ATOMS (A''2) 4.395 MAIN-CHAIN BOND REFINED ATOMS (A''2) 3.462 SIDE-CHAIN ANGLE REFINED ATOMS (A''2) 3.263 SIDE-CHAIN BOND REFINED ATOMS (A''2) 2.21 r_angle_refined_deg 2.094 r_angle_other_deg 1.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.751 r_dihedral_angle_4_deg 27.378 r_dihedral_angle_3_deg 17.914 r_dihedral_angle_1_deg 5.825 MAIN-CHAIN ANGLE REFINED ATOMS (A''2) 4.395 MAIN-CHAIN BOND REFINED ATOMS (A''2) 3.462 SIDE-CHAIN ANGLE REFINED ATOMS (A''2) 3.263 SIDE-CHAIN BOND REFINED ATOMS (A''2) 2.21 r_angle_refined_deg 2.094 r_angle_other_deg 1.136 MAIN-CHAIN BOND OTHER ATOMS (A''2) 0.59 r_symmetry_hbond_refined 0.289 r_nbtor_refined 0.217 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.213 r_nbd_other 0.206 r_symmetry_vdw_other 0.187 r_xyhbond_nbd_refined 0.152 r_nbtor_other 0.095 CHIRAL-CENTER RESTRAINTS (A''3) 0.082 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1505 Nucleic Acid Atoms 1101 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing