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CobT from Methanocaldococcus jannaschii in complex with Alpha-Ribozole 5'-Phosphate, Nicotinic Acid, and Nicotinic Acid Mononucleotide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L0Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 Crystals were formed by mixing 13.3 mg/ml protein solution containing added 1 mM 5,6-dimethylbenzimidazole and 25 mM sodium/potassium phosphate pH 7.0 with well solution containing 100 mM MES/Acetate pH 5.5, 25% PEG 1.5K. Crystals were cryoprotected in 20% ethylene glycol, 100 mM MES/Acetate buffer pH 5.5, 16% PEG 4K, 1 mM nicotinic acid mononucleotide overnight prior to freezing
Crystal Properties Matthews coefficient Solvent content 2.21 44.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.58 α = 90 b = 139 β = 111.67 c = 54.49 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 PILATUS3 X 6M 2018-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97934 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.293 47.5762 97.42 0.0646 15.5 6.9 28756
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.293 2.375 92.86 0.4771 2.53 6.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3L0Z 2.293 40.93 1.39 28689 1433 97.45 0.1956 0.1933 0.1962 0.2403 0.2411 58.7454
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5220 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 88
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building