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Structure of Rv2985, a Nudix diadenosine polyphosphatase from M. tuberculosis, in complex with putative ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 0.1 M bis-tris (pH 6.0), 32.8% PEG 3350, 5 mM Ap4A, and 6.3 mg/mL of Rv2985(HT)
Crystal Properties Matthews coefficient Solvent content 2.7 54.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.005 α = 90 b = 119.005 β = 90 c = 115.211 γ = 90
Symmetry Space Group P 4 21 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 EIGER X 16M 2024-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979338 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.527 33.977 99.92 0.998 7.3 13.6 28319 58.67
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.527 2.571 0.347
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.53 33.977 1.33 28298 1993 99.84 0.2382 0.2344 0.2343 0.2898 0.2897 65
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.5955 f_angle_d 0.6147 f_chiral_restr 0.043 f_plane_restr 0.0055 f_bond_d 0.0031
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4450 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 111
Software Software Software Name Purpose PHENIX refinement Coot model building autoPROC data scaling PHENIX phasing Aimless data scaling pointless data scaling STARANISO data scaling XDS data reduction