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Crystal structure of transcriptional regulator (NrpR) from Streptococcus salivarius K12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 295 0.1 M Bis-Tris propane (pH 7.95), 0.7 M Sodium Citrate tribasic dihydrate
Crystal Properties Matthews coefficient Solvent content 2.33 47.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.747 α = 90 b = 128.26 β = 100.616 c = 72.63 γ = 90
Symmetry Space Group I 1 2 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 EIGER X 9M 2022-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.9797 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.59 36.705 97.4 0.99 11.8 2.5 9474
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.59 2.71 0.95
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 MOLECULAR REPLACEMENT FREE R-VALUE 2.59 36.705 9474 458 97.199 0.187 0.1834 0.1908 0.2659 0.2782 76.112
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] -0.05 -0.017 0.011 0.042
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.21 r_dihedral_angle_3_deg 17.895 r_dihedral_angle_4_deg 16.789 r_lrange_it 16.507 r_lrange_other 16.502 r_scangle_it 10.258 r_scangle_other 10.255 r_mcangle_other 9.576 r_mcangle_it 9.575 r_scbond_it 6.737
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.21 r_dihedral_angle_3_deg 17.895 r_dihedral_angle_4_deg 16.789 r_lrange_it 16.507 r_lrange_other 16.502 r_scangle_it 10.258 r_scangle_other 10.255 r_mcangle_other 9.576 r_mcangle_it 9.575 r_scbond_it 6.737 r_mcbond_it 6.735 r_scbond_other 6.734 r_mcbond_other 6.706 r_dihedral_angle_1_deg 6.127 r_angle_refined_deg 1.454 r_angle_other_deg 1.239 r_symmetry_xyhbond_nbd_refined 0.248 r_nbd_other 0.24 r_nbd_refined 0.204 r_symmetry_nbd_other 0.201 r_symmetry_nbd_refined 0.19 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.155 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2378 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing