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Crystal structure of Sco3205, a MarR family transcriptional regulator from Streptomyces coelicolor, in complex with DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZMD PDB ENTRY 3ZMD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 20-40% (V/V) MPD, 80-100 MM SODIUM ACETATE AND 50 MM MES PH 5.6
Crystal Properties Matthews coefficient Solvent content 3.93 72.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.8 α = 90 b = 70.8 β = 90 c = 557.48 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2011-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 Diamond I24
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 69.68 96 0.1 13.7 8.7 37192 80.9
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 2.87 78.2 0.37 1.9 3
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 3ZMD 2.8 59.88 35209 1848 95.97 0.17668 0.17565 0.1769 0.19649 0.197 RANDOM 60.9
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] 0.54 0.54 -1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.533 r_dihedral_angle_4_deg 19.479 r_dihedral_angle_3_deg 19.398 r_dihedral_angle_1_deg 5.59 r_mcangle_it 2.078 r_scbond_it 1.571 r_angle_other_deg 1.435 r_angle_refined_deg 1.351 r_mcbond_it 1.311 r_mcbond_other 1.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.533 r_dihedral_angle_4_deg 19.479 r_dihedral_angle_3_deg 19.398 r_dihedral_angle_1_deg 5.59 r_mcangle_it 2.078 r_scbond_it 1.571 r_angle_other_deg 1.435 r_angle_refined_deg 1.351 r_mcbond_it 1.311 r_mcbond_other 1.311 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_bond_other_d 0.005 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it 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 4933 Nucleic Acid Atoms 1792 Solvent Atoms 14 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing