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Structure of the B3 DNA-Binding Domain of NGA1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LDU 4lduA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 Reservoir solution:
0.1 M HEPES-NaOH pH 7.5,
0.2 M potassium sodium tartrate,
1.6 M potassium-sodium phosphate,
5% PEG 4000.
Protein concentration: 7.1 mg/ml.
Drop: 0.4 microL protein solution + 0.2 microL reservoir solution.
Crystal Properties Matthews coefficient Solvent content 1.97 37.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.758 α = 90 b = 151.179 β = 90 c = 47.513 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2017-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9763 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 75.59 99.22 0.0186 0.999 21.81 2 39391 17.75
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.864 98 0.1059 0.971 6.85 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4lduA 1.8 75.59 1.39 39391 3911 99.22 0.1529 0.1482 0.1573 0.1948 0.2018
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.599 f_angle_d 1.53 f_chiral_restr 0.11 f_bond_d 0.019 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1872 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling MoRDa phasing