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Crystal structure of an acetate kinase from Mycobacterium smegmatis bound to AMP and sulfate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3R9P PDB entry 3r9p
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 MysmA.00640.a.A1 PS00601 at 20 mg/mL with 2 mM AMP and 2 mM MnCl2 against JCSG+ condition H7, 25% PEG 3350, 0.1 M BisTris, 0.2 M ammonium sulfate with 15% ethylene glycol as cryo-protectant, crystal tracking ID 238414h7, unique puck ID gpy2-6, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.53 51.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.43 α = 90 b = 81.91 β = 96.51 c = 95.4 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 RIGAKU SATURN 944+ VariMax 2012-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 1.7 50 97.9 0.045 20.66 4.6 93194 91223 -3 23.913
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 1.7 1.74 90.2 0.29 3.22
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 3r9p 1.7 45.74 91201 4566 97.89 0.1747 0.1733 0.183 0.2015 0.2068 RANDOM 19.5464
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] -0.8 -0.67 0.43 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.396 r_dihedral_angle_4_deg 18.301 r_dihedral_angle_3_deg 11.906 r_dihedral_angle_1_deg 6.414 r_angle_refined_deg 1.484 r_mcangle_it 1.275 r_mcbond_it 0.777 r_mcbond_other 0.776 r_angle_other_deg 0.775 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.396 r_dihedral_angle_4_deg 18.301 r_dihedral_angle_3_deg 11.906 r_dihedral_angle_1_deg 6.414 r_angle_refined_deg 1.484 r_mcangle_it 1.275 r_mcbond_it 0.777 r_mcbond_other 0.776 r_angle_other_deg 0.775 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5570 Nucleic Acid Atoms Solvent Atoms 697 Heterogen Atoms 68
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction