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Crystal structure of ChbG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I5I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 15% (v/v) PEG 550 MME, 0.1M MES pH6.5
Crystal Properties Matthews coefficient Solvent content 2.39 48.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.23 α = 90 b = 67.03 β = 90 c = 146.4 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 125 PIXEL DECTRIS EIGER X 9M 2020-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.9794 PAL/PLS 5C (4A)
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 1.83 28.51 99 0.1074 0.999 16.48 12.1 47465
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 1.83 1.895 1.96 0.722
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2I5I 1.83 28.51 47459 2373 99.003 0.222 0.2203 0.2032 0.2569 0.2511 26.373
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] 0.078 0.103 -0.181
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.315 r_dihedral_angle_4_deg 18.144 r_dihedral_angle_3_deg 14.278 r_dihedral_angle_1_deg 6.026 r_lrange_other 5.562 r_lrange_it 5.561 r_scangle_it 5.331 r_scangle_other 5.33 r_scbond_it 4.352 r_scbond_other 4.351
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.315 r_dihedral_angle_4_deg 18.144 r_dihedral_angle_3_deg 14.278 r_dihedral_angle_1_deg 6.026 r_lrange_other 5.562 r_lrange_it 5.561 r_scangle_it 5.331 r_scangle_other 5.33 r_scbond_it 4.352 r_scbond_other 4.351 r_mcangle_other 3.645 r_mcangle_it 3.644 r_mcbond_it 3.19 r_mcbond_other 3.178 r_angle_other_deg 2.321 r_angle_refined_deg 1.707 r_xyhbond_nbd_refined 0.233 r_symmetry_nbd_other 0.219 r_nbd_refined 0.218 r_nbd_other 0.199 r_nbtor_refined 0.182 r_symmetry_nbd_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.158 r_symmetry_xyhbond_nbd_other 0.146 r_chiral_restr 0.101 r_symmetry_nbtor_other 0.072 r_bond_other_d 0.036 r_bond_refined_d 0.014 r_gen_planes_refined 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3885 Nucleic Acid Atoms Solvent Atoms 388 Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing