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Ancestral protein AncThEn of Phosphomethylpyrimidine kinases family
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JXH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 Protein condition: Protein 20 mg/mL, HMP 1 mM, ADP 1 mM, HEPES 50 mM pH 8.0, NaCl 150 mM and 2-mercaptoethanol 5 mM
Reservoir condition: 2-Propanol 14% v/v, Calcium chloride dihydrate 0.14 M, Sodium acetate 0.07 M, Glycerol 30% v/v.
Crystal Properties Matthews coefficient Solvent content 2.96 58.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.316 α = 90 b = 113.316 β = 90 c = 112.233 γ = 90
Symmetry Space Group P 42 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 PILATUS 2M 2019-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.45867 LNLS W01B-MX2
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 3.2 45.96 99.83 0.41 0.4181 0.08148 0.996 10.88 25.8 12568 82.69
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 3.2 3.314 99.92 3.331 3.394 0.6455 0.544 1.27 27.3
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 1JXH 3.2 45.96 1.33 12555 606 99.9 0.2332 0.2322 0.2342 0.2539 0.2584 81.42
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 15.2155 f_angle_d 0.9754 f_chiral_restr 0.0643 f_plane_restr 0.0061 f_bond_d 0.0056
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3099 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 10
Software Software Software Name Purpose PHENIX refinement MxCuBE data collection XDS data reduction Aimless data scaling MOLREP phasing