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Crystal structure of EccC5 DUF domain of Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NP7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 25% PEG MME 2000, 0.3 M Trimethylamine N-oxide dihydrate, 0.1 M Tris pH 8
Crystal Properties Matthews coefficient Solvent content 2.17 43.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.301 α = 88.39 b = 52.236 β = 84.6 c = 57.441 γ = 80.17
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 6M 2023-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9792 ALBA XALOC
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 2.05 57.18 95.1 0.055 0.065 0.035 0.998 9.6 3.5 32869
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 2.05 2.11 0.354 0.432 0.242 0.869 2.6 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.05 57.18 32862 1645 95.1 0.1866 0.1846 0.2242 0.2316 RANDOM 34.59
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] 5.7297 -3.9873 5.8561 -9.8938 -4.6486 4.1641
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.35 t_omega_torsion 3.4 t_angle_deg 0.88 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3932 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms
Software Software Software Name Purpose BUSTER refinement PHENIX refinement Coot model building autoPROC data processing Aimless data scaling PHASER phasing