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Crystal structure of a CHAD domain from Chlorobium tepidum in complex with inorganic polyphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E0S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 298 0.4 M (NH4)3PO4
Crystal Properties Matthews coefficient Solvent content 2.47 50.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.4 α = 90 b = 97.031 β = 90 c = 106.397 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 PILATUS 2M 2018-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.999856 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 2.05 19.7 99.6 0.149 0.155 1 14.1 13.3 22776 -3 -3 46.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.17 99.6 2.26 2.35 0.43 1.05 13.2
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 3e0s 2.05 19.7 21397 1127 98.49 0.20997 0.20767 0.2142 0.25483 0.2648 RANDOM 46.982
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] 0.2 1.57 -1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.25 r_dihedral_angle_4_deg 15.736 r_dihedral_angle_3_deg 14.484 r_long_range_B_refined 8.58 r_long_range_B_other 8.418 r_dihedral_angle_1_deg 5.133 r_scangle_other 4.444 r_scbond_it 3.307 r_scbond_other 2.873 r_mcangle_it 2.529
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.25 r_dihedral_angle_4_deg 15.736 r_dihedral_angle_3_deg 14.484 r_long_range_B_refined 8.58 r_long_range_B_other 8.418 r_dihedral_angle_1_deg 5.133 r_scangle_other 4.444 r_scbond_it 3.307 r_scbond_other 2.873 r_mcangle_it 2.529 r_mcangle_other 2.528 r_mcbond_it 1.86 r_mcbond_other 1.859 r_angle_refined_deg 1.397 r_angle_other_deg 1.226 r_chiral_restr 0.064 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2493 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing