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Crystal structure of Nitrile Hydratase mutant S113A complexed with Trimethylacetamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AHJ PDB ENTRY 2ahj
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.44 49.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.606 α = 90 b = 60.012 β = 125.14 c = 81.499 γ = 90
Symmetry Space Group C 1 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 95 CCD ADSC QUANTUM 210 2008-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
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 1.66 50 99.9 0.038 13.9 52970
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 PDB ENTRY 2ahj 1.66 28.09 52970 50262 2696 99.77 0.17408 0.17269 0.1728 0.19962 0.2001 RANDOM 19.192
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.757 r_dihedral_angle_4_deg 18.043 r_dihedral_angle_1_deg 11.326 r_dihedral_angle_3_deg 10.311 r_scangle_it 2.781 r_scbond_it 1.856 r_angle_refined_deg 1.254 r_mcangle_it 1.155 r_mcbond_it 0.763 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.757 r_dihedral_angle_4_deg 18.043 r_dihedral_angle_1_deg 11.326 r_dihedral_angle_3_deg 10.311 r_scangle_it 2.781 r_scbond_it 1.856 r_angle_refined_deg 1.254 r_mcangle_it 1.155 r_mcbond_it 0.763 r_nbtor_refined 0.311 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.16 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.132 r_chiral_restr 0.087 r_metal_ion_refined 0.015 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3130 Nucleic Acid Atoms Solvent Atoms 530 Heterogen Atoms 8
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling