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Crystal structure of a bacterial ProRS with ligands
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J3L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 297 32-40% (v/v) Pentaerythritol propoxylate (5/4 PO/OH), 0.1-0.2 M KCl, 50 mM HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.85 56.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.575 α = 90 b = 77.204 β = 99.33 c = 73.965 γ = 90
Symmetry Space Group C 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 16M 2017-12-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.07 50 97.4 0.053 11.3 3.1 42784
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.07 2.13 97.5 0.197 4
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 2J3L 2.07 50 40645 2202 97.36 0.22963 0.22829 0.2346 0.25449 0.2618 RANDOM 32.453
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] 0.06 -0.16 -0.14 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.18 r_dihedral_angle_3_deg 13.462 r_dihedral_angle_4_deg 12.905 r_dihedral_angle_1_deg 6.3 r_long_range_B_refined 3.188 r_long_range_B_other 3.188 r_mcangle_it 1.708 r_mcangle_other 1.708 r_scangle_other 1.557 r_angle_refined_deg 1.259
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.18 r_dihedral_angle_3_deg 13.462 r_dihedral_angle_4_deg 12.905 r_dihedral_angle_1_deg 6.3 r_long_range_B_refined 3.188 r_long_range_B_other 3.188 r_mcangle_it 1.708 r_mcangle_other 1.708 r_scangle_other 1.557 r_angle_refined_deg 1.259 r_mcbond_it 0.972 r_mcbond_other 0.972 r_angle_other_deg 0.906 r_scbond_it 0.878 r_scbond_other 0.878 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_bond_other_d 0.006 r_gen_planes_refined 0.004 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 4377 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing