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Crystal structure of Lys154Asn mutant of mature AphA of S. typhimurium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z5G Partially refined structure of wild-type APHA (PDB code 1Z5G) with all HET atoms (HOH, MG etc.) removed and side chain of Lys154 replaced with ALA was used as the starting model. A random error of 0.2A was added to the atomic coordinates of the starting model.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 vapour diffusion sitting-drop, micro-seeding 4.7 293 PEG 6000, magnesium chloride, sodium acetate, dihydrogen phosphate , pH 4.7, vapour diffusion sitting-drop, micro-seeding, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.34 47.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.737 α = 90 b = 84.477 β = 90 c = 149.268 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 IMAGE PLATE MARRESEARCH OSMIC mirror 2004-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 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 2.24 30 94.5 0.055 13.5 3.4 40809 40671 24.77
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) 2.24 2.36 91.4 0.162 7.1 3.2 5241
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT Partially refined structure of wild-type APHA (PDB code 1Z5G) with all HET atoms (HOH, MG etc.) removed and side chain of Lys154 replaced with ALA was used as the starting model. A random error of 0.2A was added to the atomic coordinates of the starting model. 2.25 20 40554 40554 2004 94 0.151 0.1508 0.197 0.1972 random 24.29
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] 0.142 -4.802 4.659
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.09 c_scangle_it 3.2 c_mcangle_it 2.22 c_scbond_it 2.17 c_mcbond_it 1.4 c_angle_deg 1 c_improper_angle_d 0.833 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6589 Nucleic Acid Atoms Solvent Atoms 534 Heterogen Atoms 10
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling CNS refinement CCP4 data scaling TRUNCATE data scaling CNS phasing