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Structure of 6-aminohexanoate-oligomer hydrolase NylC precursor, D122G/H130Y/T267C mutant
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 7.5 283 1.4 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.2 44.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.879 α = 90 b = 144.004 β = 90 c = 129.284 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 210 2010-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 1.13 50 99.5 0.055 0.059 0.999 33.9 7 240917
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.13 1.15 98.6 0.647 0.703 0.904 3.22 6.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3AXG 1.13 28.269 238908 12072 98.538 0.13 0.1288 0.1247 0.1553 0.149 17.008
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] 2.529 -1.385 -1.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.472 r_dihedral_angle_4_deg 16.977 r_dihedral_angle_3_deg 11.194 r_dihedral_angle_1_deg 6.549 r_lrange_it 4.251 r_lrange_other 4.251 r_scangle_it 3.51 r_scangle_other 3.222 r_rigid_bond_restr 3.026 r_scbond_it 2.762
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.472 r_dihedral_angle_4_deg 16.977 r_dihedral_angle_3_deg 11.194 r_dihedral_angle_1_deg 6.549 r_lrange_it 4.251 r_lrange_other 4.251 r_scangle_it 3.51 r_scangle_other 3.222 r_rigid_bond_restr 3.026 r_scbond_it 2.762 r_scbond_other 2.555 r_mcangle_it 1.962 r_mcangle_other 1.962 r_angle_refined_deg 1.807 r_mcbond_other 1.635 r_mcbond_it 1.634 r_angle_other_deg 1.591 r_nbd_other 0.326 r_symmetry_nbd_refined 0.322 r_metal_ion_refined 0.258 r_nbd_refined 0.221 r_symmetry_nbd_other 0.198 r_symmetry_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.097 r_symmetry_xyhbond_nbd_other 0.088 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4877 Nucleic Acid Atoms Solvent Atoms 732 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing