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Crystal structure of SmbA in complex with ppGpp.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GS8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.1M amino acids, 0.1M Sodium HEPES pH 7.5, MOPS (acid),40% v/v ethylene glycol, 20%w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.65 53.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.921 α = 90 b = 58.192 β = 93.06 c = 115.253 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 2M 2016-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00004 SLS X06DA
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 3.26 49.67 99.8 0.34 0.368 0.14 0.982 6.2 6.8 22723
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 3.26 3.52 99.3 1.144 1.237 0.468 0.718 6.8
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 6GS8 3.3 30 20784 1143 99.74 0.2138 0.212 0.2151 0.2462 0.247 RANDOM 46.328
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] 2.62 -0.93 -2.84 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.735 r_dihedral_angle_3_deg 20.503 r_dihedral_angle_4_deg 18.079 r_dihedral_angle_1_deg 8.565 r_angle_other_deg 2.023 r_angle_refined_deg 1.915 r_chiral_restr 0.071 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.735 r_dihedral_angle_3_deg 20.503 r_dihedral_angle_4_deg 18.079 r_dihedral_angle_1_deg 8.565 r_angle_other_deg 2.023 r_angle_refined_deg 1.915 r_chiral_restr 0.071 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8952 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing PDB_EXTRACT data extraction