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Structure of 6-aminohexanoate-oligomer hydrolase NylC precursor, H130Y/N266A/T267A 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 2.22 44.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.242 α = 90 b = 144.345 β = 90 c = 129.178 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 270 2009-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0000 Photon Factory BL-17A
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 1.35 50 98 0.074 0.077 0.999 30.4 12.5 140625
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 1.35 1.37 82 0.499 0.526 0.94 3.35 8.7
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 1.35 37.006 140512 7049 97.716 0.112 0.1106 0.114 0.1394 0.1429 21.236
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] 1.836 -1.831 -0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.019 r_dihedral_angle_4_deg 14.717 r_dihedral_angle_3_deg 11.66 r_dihedral_angle_1_deg 6.796 r_lrange_it 3.493 r_lrange_other 3.493 r_scangle_it 3.019 r_scangle_other 2.782 r_scbond_it 2.654 r_scbond_other 2.396
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.019 r_dihedral_angle_4_deg 14.717 r_dihedral_angle_3_deg 11.66 r_dihedral_angle_1_deg 6.796 r_lrange_it 3.493 r_lrange_other 3.493 r_scangle_it 3.019 r_scangle_other 2.782 r_scbond_it 2.654 r_scbond_other 2.396 r_mcangle_it 1.913 r_mcangle_other 1.913 r_rigid_bond_restr 1.706 r_mcbond_it 1.581 r_mcbond_other 1.581 r_angle_other_deg 1.498 r_angle_refined_deg 1.492 r_symmetry_nbd_refined 0.23 r_nbd_other 0.226 r_nbd_refined 0.209 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.167 r_metal_ion_refined 0.159 r_symmetry_xyhbond_nbd_refined 0.145 r_xyhbond_nbd_refined 0.129 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4864 Nucleic Acid Atoms Solvent Atoms 579 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing