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Crystal structure of apo form of acetate kinase (AckA) from Salmonella typhimurium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IIR PDB ENTRY 2IIR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 UNDER-OIL MICROBATCH 7.5 298 0.1M HEPES, 30%(w/v) PEG 4000, 0.2M Calcium Chloride, pH 7.5, UNDER-OIL MICROBATCH, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.23 44.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 283.159 α = 90 b = 62.168 β = 93.57 c = 91.695 γ = 90
Symmetry Space Group C 1 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 IMAGE PLATE MARRESEARCH Mirror 2009-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54
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 2.7 50 96.9 0.138 2.8 43980 42614
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 2.7 2.8 84.5 0.558 2.06 1.9 4322
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2IIR 2.7 50 44122 40430 2151 96.54 0.224 0.22082 0.2187 0.28324 0.2782 RANDOM 43.703
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] -0.39 -0.19 1.03 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.157 r_dihedral_angle_4_deg 19.418 r_dihedral_angle_3_deg 15.382 r_dihedral_angle_1_deg 5.024 r_angle_refined_deg 0.977 r_scangle_it 0.756 r_scbond_it 0.43 r_mcangle_it 0.309 r_mcbond_it 0.162 r_chiral_restr 0.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.157 r_dihedral_angle_4_deg 19.418 r_dihedral_angle_3_deg 15.382 r_dihedral_angle_1_deg 5.024 r_angle_refined_deg 0.977 r_scangle_it 0.756 r_scbond_it 0.43 r_mcangle_it 0.309 r_mcbond_it 0.162 r_chiral_restr 0.066 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11736 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 16
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling