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The N-terminal domain of MerR-like protein TipAL bound to promoter DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R8D PDB ENTRY 1R8D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 SITTING DROP CONTAINING 4 MICROLITERS PROTEIN-DNA SOLUTION PLUS 6 MICROLITERS RESERVOIR SOLUTION. PROTEIN-DNA SOLUTION: 500 MICROMOLAR (6 MILLIGRAMS/MILLILITER) PROTEIN, 275 MICROMOLAR DOUBLE-STRANDED DNA, 123 MILLIMOLAR SODIUM CHLORIDE, 16 MILLIMOLAR TRIS (TRIS(HYDROXYMETHYL)AMINOMETHANE), 8 MILLIMOLAR SODIUM CACODYLATE, 4 MILLIMOLAR MAGNESIUM CHLORIDE, 0.8 MILLIMOLAR EDTA (ETHYLENEDIAMINETETRAACETIC ACID), PH 8. RESERVOIR SOLUTION: 15% (WEIGHT/VOLUME) PEG-8K (POLY(ETHYLENE GLYCOL) WITH MOLECULAR MASS 8000 GRAMS/MOLE), 200 MILLIMOLAR MAGNESIUM CHLORIDE, 100 MILLIMOLAR TRIS (TRIS(HYDROXYMETHYL)AMINOMETHANE), PH 8.5.
Crystal Properties Matthews coefficient Solvent content 2.83 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.85 α = 90 b = 67.467 β = 90 c = 73.129 γ = 90
Symmetry Space Group P 21 21 2
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 MARRESEARCH 2005-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 2.9 72.74 99.5 0.08 20.2 6.3 5321
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 2.9 3.06 99.5 0.35 5.5 6.1
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 1R8D 2.9 30 4922 230 95.9 0.24 0.239 0.2443 0.274 0.2835 RANDOM 47.66
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] 1.5 -4.37 2.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.988 r_dihedral_angle_4_deg 18.876 r_dihedral_angle_3_deg 15.313 r_dihedral_angle_1_deg 5.115 r_scangle_it 5.019 r_scbond_it 3.359 r_mcangle_it 2.385 r_mcbond_it 1.519 r_angle_refined_deg 1.337 r_angle_other_deg 0.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.988 r_dihedral_angle_4_deg 18.876 r_dihedral_angle_3_deg 15.313 r_dihedral_angle_1_deg 5.115 r_scangle_it 5.019 r_scbond_it 3.359 r_mcangle_it 2.385 r_mcbond_it 1.519 r_angle_refined_deg 1.337 r_angle_other_deg 0.912 r_symmetry_vdw_other 0.374 r_mcbond_other 0.342 r_nbd_refined 0.201 r_nbtor_refined 0.199 r_nbd_other 0.176 r_symmetry_vdw_refined 0.152 r_xyhbond_nbd_refined 0.122 r_nbtor_other 0.084 r_symmetry_hbond_refined 0.075 r_chiral_restr 0.051 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 794 Nucleic Acid Atoms 428 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing