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The Structure of DNA-binding domain of response regulator from Escherichia coli K-12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OQR PDB ENTRY 2OQR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 LITHIUM SULFATE, 0.1M HEPES PH 7.5.
Crystal Properties Matthews coefficient Solvent content 1.92 35.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.44 α = 90 b = 36.44 β = 90 c = 138.47 γ = 90
Symmetry Space Group P 43 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 IMAGE PLATE MARRESEARCH 2009-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR-H
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 2.5 50 95 0.06 19 4.1 3378 2 40.12
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 2.5 35 77.7 0.1 9.1 3.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2OQR 2.52 35.24 3142 315 97.05 0.24079 0.23649 0.28307 0.3031 RANDOM 26.763
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 -1 1.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.861 r_dihedral_angle_4_deg 23.903 r_dihedral_angle_3_deg 20.665 r_dihedral_angle_1_deg 6.972 r_scangle_it 1.749 r_angle_refined_deg 1.664 r_scbond_it 1.248 r_symmetry_hbond_refined 0.613 r_mcangle_it 0.604 r_mcbond_it 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.861 r_dihedral_angle_4_deg 23.903 r_dihedral_angle_3_deg 20.665 r_dihedral_angle_1_deg 6.972 r_scangle_it 1.749 r_angle_refined_deg 1.664 r_scbond_it 1.248 r_symmetry_hbond_refined 0.613 r_mcangle_it 0.604 r_mcbond_it 0.44 r_nbtor_refined 0.321 r_symmetry_vdw_refined 0.238 r_nbd_refined 0.234 r_xyhbond_nbd_refined 0.175 r_chiral_restr 0.124 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 825 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing