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Crystal structure of cytidylate kinase from Mycobacterium smegmatis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3R8C PDB ENTRY 3R8C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 MysmA.00663.a.A1 PS00600 at 37.2 mg/mL against JCSG+ screen condition E2. 0.2 M NaCl, 0.1 M sodium cacodylate pH 6.5, 2 M ammonium sulfate with 25% ethylene glycol as cryo-protectant, crystal tracking ID 215891e2, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.41 48.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.22 α = 90 b = 96.22 β = 90 c = 43.15 γ = 120
Symmetry Space Group P 3 2 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 CCD ADSC QUANTUM 315r 2011-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97946 ALS 5.0.1
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 50 98.8 0.072 21.82 7.8 15827 15632 -3 28.667
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 2.05 94.2 0.416 3.94 5.2 1182
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3R8C 2 50 15571 776 98.39 0.1705 0.1683 0.1812 0.21 0.226 RANDOM 24.2344
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] -0.94 -0.47 -0.94 1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.9 r_dihedral_angle_4_deg 18.829 r_dihedral_angle_3_deg 10.841 r_dihedral_angle_1_deg 4.781 r_scangle_it 3.647 r_scbond_it 2.187 r_angle_refined_deg 1.341 r_mcangle_it 1.212 r_mcbond_it 0.692 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.9 r_dihedral_angle_4_deg 18.829 r_dihedral_angle_3_deg 10.841 r_dihedral_angle_1_deg 4.781 r_scangle_it 3.647 r_scbond_it 2.187 r_angle_refined_deg 1.341 r_mcangle_it 1.212 r_mcbond_it 0.692 r_chiral_restr 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1572 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 19
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction