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Structure of the Salmonella tRNA pyrophosphokinase CapRel
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6S2T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277.16 peg 20000, 20%
Crystal Properties Matthews coefficient Solvent content 2.39 48.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.573 α = 90 b = 136.196 β = 102.7 c = 57.782 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 EIGER X 16M 2021-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97856 SOLEIL PROXIMA 1
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 2.312 68.1 91.9 0.115 0.124 0.046 0.998 11.2 7.1 20877 59.56
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.312 2.61 1.292 0.531 1.5
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 6S2T 2.312 68.1 20877 1065 63.9 0.2145 0.2118 0.203 0.2648 0.2594 RANDOM 68.66
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] -7.6132 1.147 5.0095 2.6037
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.86 t_omega_torsion 2.73 t_angle_deg 0.97 t_bond_d 0.008 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 18.86 t_omega_torsion 2.73 t_angle_deg 0.97 t_bond_d 0.008 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 5304 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 3
Software Software Software Name Purpose BUSTER refinement autoPROC data reduction Aimless data scaling PHASER phasing