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Structure of the catalytic domain of T. thermophilus Rel in complex with AMP and ppGpp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VJ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.002 M Zinc chloride 0.1 M Tris 8.0 20 % w/v PEG 6000
Crystal Properties Matthews coefficient Solvent content 3 58.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.739 α = 90 b = 50.346 β = 111 c = 86.057 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 9M 2016-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9801 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.95 56.36 91.9 0.12 0.04 0.996 13.8 10.3 6572 102.64
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.95 3.02 1.1 0.36 0.868
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 1vj7 2.95 56.36 6572 330 63.2 0.216 0.214 0.2356 0.248 0.274 RANDOM 101.56
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] -3.5954 13.1263 0.4492 3.1462
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.46 t_omega_torsion 2.56 t_angle_deg 1.17 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.46 t_omega_torsion 2.56 t_angle_deg 1.17 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2594 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 67
Software Software Software Name Purpose BUSTER refinement XDS data reduction autoPROC data scaling Rosetta phasing