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Structure of the N-terminal catalytic region of T. thermophilus Rel bound to 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 7.5 277 0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M
Sodium citrate tribasic dihydrate; 0.2M Sodium potassium
tartrate tetrahydrate; 0.2M Sodium oxamate,
Sodium HEPES; MOPS (acid) pH 7.5, 25% v/v MPD; 25% PEG 1000; 25% w/v
PEG 3350
Crystal Properties Matthews coefficient Solvent content 4.44 72.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.927 α = 90 b = 87.927 β = 90 c = 184.252 γ = 90
Symmetry Space Group P 41 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 EIGER2 X 9M 2016-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98012 SOLEIL PROXIMA 2
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 2.75 92.13 99.8 0.16 0.204 0.041 0.999 13.7 24.8 14292 90.9
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 2.75 2.9 98.9 2.452 2.508 0.522 0.627 22.6
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 2.75 62.17 14116 716 72 0.197 0.196 0.204 0.22 0.2336 RANDOM 81.28
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] 4.9952 4.9952 -9.9904
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.82 t_omega_torsion 2.35 t_angle_deg 1.1 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.82 t_omega_torsion 2.35 t_angle_deg 1.1 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle 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 2731 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 52
Software Software Software Name Purpose BUSTER refinement XDS data reduction autoPROC data scaling Rosetta phasing