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Structure of 6-Aminohexanoate-dimer Hydrolase, S112A/G181D Mutant Complexed with 6-Aminohexanoate-dimer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DCF PDB ENTRY 2DCF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 283 2.2M ammonium sulfate, 0.2M lithium sulfate, 0.1M MES, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 3.56 65.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.684 α = 90 b = 96.684 β = 90 c = 113.164 γ = 120
Symmetry Space Group P 32 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 CCD RIGAKU JUPITER 210 2005-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.9000 SPring-8 BL38B1
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 1.6 50 100 0.063 38.45 10.9 81044 81044 -3 15.9
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 1.6 1.66 99.9 0.435 3.98 10.2 7973
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 2DCF 1.6 31.65 79428 7961 98 0.172 0.172 0.1725 0.187 0.1868 RANDOM 18.6
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] 0.56 0.41 0.56 -1.12
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.9 c_scangle_it 2.53 c_scbond_it 1.71 c_mcangle_it 1.63 c_mcbond_it 1.09 c_angle_deg 0.9 c_improper_angle_d 0.68 c_bond_d 0.004 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.9 c_scangle_it 2.53 c_scbond_it 1.71 c_mcangle_it 1.63 c_mcbond_it 1.09 c_angle_deg 0.9 c_improper_angle_d 0.68 c_bond_d 0.004 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2962 Nucleic Acid Atoms Solvent Atoms 441 Heterogen Atoms 79
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing