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Crystal structure of CMGC family protein kinase from Trichomonas vaginalis (AMP-PNP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XVU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 291 JCSG+ B7: 0.10 M Sodium acetate, pH 4.6, 8.0% (w/v) PEG 4000, TrvaA.01010.a.B1.PW39249 at 16.4 mg/mL. 2mM AMP-PNP and 2mM MgCl2 added prior to crystallization. No Mg bound. plate 13860 well B7 drop 2. Puck: PSL-0807, Cryo: 25% PEG 200 + 75% crystallant.
Crystal Properties Matthews coefficient Solvent content 2.62 53.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.554 α = 90 b = 108.124 β = 90 c = 41.554 γ = 90
Symmetry Space Group P 21 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 EIGER2 XE 9M 2024-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9786 NSLS-II 19-ID
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 2.1 108.12 99.9 0.115 0.122 0.039 0.995 9.9 9.9 23781
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 2.1 2.15 99.8 1.314 1.381 0.416 0.816 10.4
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 2.1 54.06 1.34 23711 1127 99.69 0.2017 0.1994 0.2024 0.2459 0.2424
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 16.132 f_angle_d 1.01 f_chiral_restr 0.051 f_bond_d 0.009 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2407 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 31
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing