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1.8 Angstrom Resolution Crystal Structure of Diaminopimelate Decarboxylase (lysA) from Vibrio cholerae.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P3E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 Protein solution: 7.8 mg/mL, 0.25M Sodium chloride, 0.01M Tris pH 8.3; Screen solution: PACT (D8) 0.2M Ammonium chloride, 0.1M Tris pH 8.0, 20%(w/v) PEG6000., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.12 42.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.394 α = 105.31 b = 80.329 β = 93.62 c = 118.693 γ = 90.52
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 MARMOSAIC 300 mm CCD Beryllium lenses 2010-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 1.8 30 97.5 0.048 17.4 2.6 147832 147832 -3 28.3
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) 1.8 1.83 96.2 0.363 2.7 2.6 7354
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 (All) 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 2P3E 1.8 29.94 138491 138491 7289 97.51 0.18449 0.18449 0.18266 0.188 0.21874 0.2235 RANDOM 31.855
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] 1.51 0.34 -0.25 -2.98 -1.49 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.451 r_dihedral_angle_4_deg 13.373 r_dihedral_angle_3_deg 9.495 r_scangle_it 4.63 r_dihedral_angle_1_deg 3.243 r_scbond_it 2.928 r_mcangle_it 2.072 r_angle_refined_deg 1.392 r_mcbond_it 1.214 r_angle_other_deg 0.846
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.451 r_dihedral_angle_4_deg 13.373 r_dihedral_angle_3_deg 9.495 r_scangle_it 4.63 r_dihedral_angle_1_deg 3.243 r_scbond_it 2.928 r_mcangle_it 2.072 r_angle_refined_deg 1.392 r_mcbond_it 1.214 r_angle_other_deg 0.846 r_mcbond_other 0.327 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12599 Nucleic Acid Atoms Solvent Atoms 1121 Heterogen Atoms 4
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling