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Crystal structure of Nitrile Hydratase 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 2.45 49.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.963 α = 90 b = 60.177 β = 125.49 c = 81.83 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 2008-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 1.000 Photon Factory BL-6A
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 1.46 50 93.3 0.042 17.1 71422
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 1.47 27.51 71422 67709 3596 92.52 0.19191 0.19013 0.1881 0.22597 0.2229 RANDOM 20.674
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 33.407 r_dihedral_angle_4_deg 18.402 r_dihedral_angle_1_deg 10.769 r_dihedral_angle_3_deg 10.489 r_scangle_it 2.446 r_scbond_it 1.607 r_angle_refined_deg 1.21 r_mcangle_it 1.053 r_mcbond_it 0.675 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.407 r_dihedral_angle_4_deg 18.402 r_dihedral_angle_1_deg 10.769 r_dihedral_angle_3_deg 10.489 r_scangle_it 2.446 r_scbond_it 1.607 r_angle_refined_deg 1.21 r_mcangle_it 1.053 r_mcbond_it 0.675 r_nbtor_refined 0.309 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.178 r_symmetry_hbond_refined 0.107 r_xyhbond_nbd_refined 0.105 r_chiral_restr 0.083 r_metal_ion_refined 0.04 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3203 Nucleic Acid Atoms Solvent Atoms 727 Heterogen Atoms 8
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling