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DNA-binding domain of CggR in complex with the DNA operator
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 290 10% (w/v) PEG 3350, 100mM MES, pH 6.5, 100mM calcium chloride, 13% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 2.07 40.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.972 α = 90 b = 103.141 β = 90.537 c = 51.111 γ = 90
Symmetry Space Group P 1 21 1
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 2020-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9797 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 50 96.8 0.086 0.998 9.4 2.3 34417 46.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.23 95.4 1.111 0.514 1.1 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.101 45.837 32691 1726 98.169 0.21 0.208 0.2192 0.2527 0.2615 43.543
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] -0.001 -0.007 -0.002 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.54 r_dihedral_angle_4_deg 20.05 r_dihedral_angle_3_deg 15.226 r_lrange_it 8.281 r_lrange_other 8.28 r_scangle_it 6.351 r_scangle_other 6.35 r_dihedral_angle_1_deg 5.35 r_mcangle_it 4.705 r_mcangle_other 4.704
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.54 r_dihedral_angle_4_deg 20.05 r_dihedral_angle_3_deg 15.226 r_lrange_it 8.281 r_lrange_other 8.28 r_scangle_it 6.351 r_scangle_other 6.35 r_dihedral_angle_1_deg 5.35 r_mcangle_it 4.705 r_mcangle_other 4.704 r_scbond_it 4.234 r_scbond_other 4.233 r_mcbond_it 3.314 r_mcbond_other 3.314 r_angle_other_deg 2.192 r_angle_refined_deg 1.336 r_nbd_other 0.356 r_symmetry_xyhbond_nbd_refined 0.233 r_symmetry_nbd_other 0.229 r_symmetry_nbd_refined 0.21 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.181 r_nbtor_refined 0.171 r_metal_ion_refined 0.158 r_symmetry_nbtor_other 0.069 r_chiral_restr 0.068 r_bond_other_d 0.028 r_symmetry_xyhbond_nbd_other 0.012 r_gen_planes_other 0.009 r_gen_planes_refined 0.008 r_bond_refined_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3045 Nucleic Acid Atoms 1950 Solvent Atoms 139 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling SHELXDE phasing