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Ancestral protein AncEn of Phosphomethylpyrimidine kinases family
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JXH 1JXH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 292 Protein condition: Protein 20 mg/mL, HEPES 50 mM pH 8.0, NaCl 150 mM and 2-mercaptoethanol 5 mM
Reservoir condition: Potassium sodium tartrate 0.8 M, Tris 0.1 M pH 8.0, PEG-MME 5000 0.5% v/v
Crystal Properties Matthews coefficient Solvent content 3.58 65.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.451 α = 90 b = 78.451 β = 90 c = 142.973 γ = 90
Symmetry Space Group P 43 2 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 2.298 36.15 99.77 0.08904 0.0909 0.01809 1 26.96 25 20580 55.41
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 2.298 2.38 1.648 1.683 0.338 0.826 1.91
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1JXH 2.3 36.15 1.36 20571 1029 99.79 0.2046 0.2036 0.2236 0.2097 69.57
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 14.5043 f_angle_d 0.5178 f_chiral_restr 0.0431 f_plane_restr 0.0042 f_bond_d 0.0023
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1636 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 24
Software Software Software Name Purpose PHENIX refinement MxCuBE data collection XDS data reduction Aimless data scaling MOLREP phasing