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Crystal structure of a cytidylate kinase CmK from Mycobacterium abscessus bound to cytidine-5'-monophosphate
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 MyabA.00663.a.A1 PW30208 at 27.9 mg/mL with 4 mM C5P and 4 mM ADP against JCSG+ screen condition E1, 0.1 M sodium cacodylate pH 6.5, 1 M trisodium citrate with 25% ethylene glycol as cryo-protectant, crystal tracking ID 220703e1, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.8 56.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.76 α = 90 b = 96.52 β = 97.22 c = 78.79 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 CCD ADSC QUANTUM 315r 2011-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.976 ALS 5.0.3
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 2.65 50 98.6 0.086 16.56 4.3 30667 30247 -3 42.885
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 2.65 2.72 98.2 0.541 3.07
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 2.65 50 30247 1520 98.64 0.233 0.231 0.2336 0.27 0.2717 RANDOM 39.0239
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] -3.02 -0.08 -0.66 3.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.981 r_dihedral_angle_4_deg 21.774 r_dihedral_angle_3_deg 13.607 r_dihedral_angle_1_deg 4.997 r_angle_refined_deg 1.472 r_angle_other_deg 1.182 r_chiral_restr 0.068 r_bond_refined_d 0.01 r_bond_other_d 0.005 r_gen_planes_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.981 r_dihedral_angle_4_deg 21.774 r_dihedral_angle_3_deg 13.607 r_dihedral_angle_1_deg 4.997 r_angle_refined_deg 1.472 r_angle_other_deg 1.182 r_chiral_restr 0.068 r_bond_refined_d 0.01 r_bond_other_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5758 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 104
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction