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Structure of 6-aminohexanoate-oligomer hydrolase from Arthrobacter sp. KI72.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AXG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.2-2.2M ammonium sulphate, 0.2M NaCl, 0.1M HEPES buffer pH 7.5-8.5
Crystal Properties Matthews coefficient Solvent content 2.24 45.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.844 α = 90 b = 144.903 β = 90 c = 129.045 γ = 90
Symmetry Space Group C 2 2 21
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 ADSC QUANTUM 315 2006-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
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 99.5 0.055 30.4 6.9 86374 -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 1.6 1.64 96.3 0.451 3.45 5.9
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 3AXG 1.6 50 81795 4316 98.88 0.16238 0.16081 0.1738 0.19239 0.2055 RANDOM 20.042
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] 2.11 -1.46 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.151 r_dihedral_angle_4_deg 14.729 r_dihedral_angle_3_deg 13.28 r_dihedral_angle_1_deg 7.105 r_scangle_it 6.569 r_scbond_it 4.614 r_mcangle_it 3.26 r_mcbond_it 2.091 r_angle_refined_deg 1.514 r_chiral_restr 0.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.151 r_dihedral_angle_4_deg 14.729 r_dihedral_angle_3_deg 13.28 r_dihedral_angle_1_deg 7.105 r_scangle_it 6.569 r_scbond_it 4.614 r_mcangle_it 3.26 r_mcbond_it 2.091 r_angle_refined_deg 1.514 r_chiral_restr 0.134 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4847 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing