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Crystal structure of CcbD complexed with PCP domain of CcbZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 0.2 M sodium acetate trihydrate, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.63 53.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.14 α = 90 b = 98.956 β = 90 c = 123.312 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 PILATUS3 S 6M 2021-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11595 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.66 123.31 100 0.073 0.079 0.03 1 20.2 13.3 124814
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.66 1.69 100 1.676 1.812 0.683 0.677 1.5 13.5
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 SIRAS FREE R-VALUE 1.66 77.297 124722 6410 99.994 0.186 0.1841 0.1827 0.2141 0.2124 31.71
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] 1.563 -0.944 -0.619
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.589 r_dihedral_angle_4_deg 19.114 r_dihedral_angle_3_deg 14.6 r_dihedral_angle_other_3_deg 13.898 r_lrange_it 7.561 r_lrange_other 7.542 r_dihedral_angle_1_deg 5.91 r_scangle_it 5.506 r_scangle_other 5.506 r_mcangle_it 4.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.589 r_dihedral_angle_4_deg 19.114 r_dihedral_angle_3_deg 14.6 r_dihedral_angle_other_3_deg 13.898 r_lrange_it 7.561 r_lrange_other 7.542 r_dihedral_angle_1_deg 5.91 r_scangle_it 5.506 r_scangle_other 5.506 r_mcangle_it 4.312 r_mcangle_other 4.312 r_scbond_it 3.754 r_scbond_other 3.753 r_mcbond_it 3.043 r_mcbond_other 3.037 r_angle_refined_deg 1.654 r_angle_other_deg 1.5 r_nbd_refined 0.219 r_symmetry_nbd_other 0.181 r_symmetry_nbd_refined 0.179 r_nbd_other 0.175 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.131 r_symmetry_xyhbond_nbd_refined 0.104 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6515 Nucleic Acid Atoms Solvent Atoms 622 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling SHELX phasing