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Transcription activator structure reveals redox control of a replication initiation reaction
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DTO PDB ENTRY 1DTO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 PROTEIN WAS CRYSTALLISED FROM 0.1 M TRIS-HCL PH 8.5, 0.3 M NACL AND 18-22% TERTIARY BUTANOL, USING THE HANGING DROP METHOD OF VAPOUR DIFFUSION.
Crystal Properties Matthews coefficient Solvent content 2.71 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.539 α = 90 b = 61.539 β = 90 c = 236.317 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD ADSC CCD 2004-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2.8 25 99.2 0.06 32 7.3 7171 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 2.8 2.9 92.1 0.5 3.5 5.8
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1DTO 2.8 24.33 6594 500 100 0.236 0.233 0.2337 0.281 RANDOM 78.02
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] -3.01 -1.5 -3.01 4.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.296 r_dihedral_angle_3_deg 16.991 r_dihedral_angle_4_deg 9.164 r_dihedral_angle_1_deg 5.616 r_scangle_it 2.438 r_scbond_it 1.45 r_angle_refined_deg 1.018 r_mcangle_it 0.89 r_mcbond_it 0.441 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.296 r_dihedral_angle_3_deg 16.991 r_dihedral_angle_4_deg 9.164 r_dihedral_angle_1_deg 5.616 r_scangle_it 2.438 r_scbond_it 1.45 r_angle_refined_deg 1.018 r_mcangle_it 0.89 r_mcbond_it 0.441 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.246 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.131 r_symmetry_hbond_refined 0.117 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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_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 1578 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing