☰ Navigation Tabs
DNA-binding domain of DeoR in complex with the DNA operator
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2W48
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 0.03 M NaNO3, 0.03 M Na2HPO4, 0.03 M (NH4)2SO4, 0.1 M Trizma base/bicine buffer system, pH 8.5, 12.5% (v/v) 2-methyl 2,4 pentanediol, 12.5% (v/v) PEG 1,000, and 12.5% (v/v) PEG 3,350
Crystal Properties Matthews coefficient Solvent content 3.38 63.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.836 α = 90 b = 96.836 β = 90 c = 81.966 γ = 90
Symmetry Space Group P 42 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 PIXEL DECTRIS PILATUS 6M 2018-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 2.3 43.34 99.6 0.144 0.151 0.999 14.08 10.86 17897 56.336
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.44 98.9 1.952 2.086 0.552 1.03 8.153
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 2W48 2.3 43.34 16949 892 99.26 0.2091 0.2064 0.2128 0.2639 0.2759 RANDOM 54.464
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] -0.04 -0.04 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.995 r_dihedral_angle_4_deg 20.414 r_dihedral_angle_3_deg 20.281 r_dihedral_angle_1_deg 5.145 r_angle_other_deg 2.337 r_angle_refined_deg 1.609 r_chiral_restr 0.074 r_bond_other_d 0.031 r_gen_planes_other 0.012 r_bond_refined_d 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.995 r_dihedral_angle_4_deg 20.414 r_dihedral_angle_3_deg 20.281 r_dihedral_angle_1_deg 5.145 r_angle_other_deg 2.337 r_angle_refined_deg 1.609 r_chiral_restr 0.074 r_bond_other_d 0.031 r_gen_planes_other 0.012 r_bond_refined_d 0.01 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1354 Nucleic Acid Atoms 609 Solvent Atoms 70 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing