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CCAAT-binding complex and HapX bound to Aspergillus nidulans cccA DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Y37 6Y37, 5VPE experimental model PDB 5VPE 6Y37, 5VPE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M ammonium fluoride, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 3.26 62.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.15 α = 90 b = 133.15 β = 90 c = 199.79 γ = 90
Symmetry Space Group I 2 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 100 PIXEL DECTRIS EIGER X 16M 2019-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 3.4 47 99.6 0.058 14.7 5.2 14326
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 3.4 3.5 99.9 0.527 2.8 5.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6Y37, 5VPE 3.4 30 13590 716 99.44 0.2544 0.2521 0.2536 0.2966 0.2798 RANDOM 136.643
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] -2.44 8.72 -6.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.827 r_dihedral_angle_3_deg 14.696 r_dihedral_angle_4_deg 10.847 r_dihedral_angle_1_deg 4.405 r_angle_other_deg 1.134 r_angle_refined_deg 1.022 r_chiral_restr 0.173 r_gen_planes_refined 0.004 r_bond_refined_d 0.002 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.827 r_dihedral_angle_3_deg 14.696 r_dihedral_angle_4_deg 10.847 r_dihedral_angle_1_deg 4.405 r_angle_other_deg 1.134 r_angle_refined_deg 1.022 r_chiral_restr 0.173 r_gen_planes_refined 0.004 r_bond_refined_d 0.002 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3533 Nucleic Acid Atoms 1517 Solvent Atoms Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing