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Crystal structure of dihydrodipicolinate synthase from aquifex aeolicus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O5K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 8 291 0.4M NaH2PO4, 1.6M K2HPO4, imidazole, 0.2M NaCl, pH 8.0, LIQUID DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.18 61.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.321 α = 90 b = 146.953 β = 109.35 c = 97.877 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 180 CCD RIGAKU JUPITER 210 2006-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.00 SPring-8 BL26B2
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 1.9 40 99.7 0.091 5.4 126980 126980 2 2 13.9
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) 1.9 1.97 98.6 0.465 4.9 12562
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 1o5k 1.9 19.76 126980 123309 3739 96.6 0.21 0.21 0.2089 0.23 0.2286 RANDOM 20.4
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] -0.94 -2.07 -0.31 1.25
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22 c_scangle_it 3.41 c_scbond_it 2.3 c_mcangle_it 1.68 c_angle_deg 1.4 c_mcbond_it 1.16 c_improper_angle_d 0.86 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9092 Nucleic Acid Atoms Solvent Atoms 489 Heterogen Atoms 10
Software Software Software Name Purpose CNS refinement BSS data collection HKL-2000 data reduction HKL-2000 data scaling CCP4 phasing